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/7769623/working'
mkdir: created directory `/scratch/stefan/7769623/working/protonate'
Storing results in /scratch/stefan/7769623/finished
Working in /scratch/stefan/7769623/working
/scratch/stefan/7769623/working /scratch/stefan/7769623

/scratch/stefan/7769623/working/protonate /scratch/stefan/7769623/working /scratch/stefan/7769623
Precomputing protomers for all compounds (pH: 7.4)
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
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
chmod: changing permissions of `/nfs/home/stefan/.install4j': No such file or directory
ph 7.4: 1134 protomers created
Coalesing and merging protomers
1085 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1095 protomers after new stereo-center expansion
/scratch/stefan/7769623/working /scratch/stefan/7769623

Bulk generating 3D conformations all protomers in /scratch/stefan/7769623/working/3D
mkdir: created directory `/scratch/stefan/7769623/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7769623/working/protonate/xaaaabq-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'
1096 3D conformations generated for 1000 compounds

Building REAL300000042001
mkdir: created directory `/scratch/stefan/7769623/working/building'
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042001'
/scratch/stefan/7769623/working/building/REAL300000042001 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042001

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042001/0 /scratch/stefan/7769623/working/building/REAL300000042001 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1
`/scratch/stefan/7769623/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC=C([N+](=O)[O-])C=C23)=C1)

`REAL300000042001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042001 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC=C([N+](=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 48, 48, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 13, 47, 89, 89, 89, 89, 89, 1] 89
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 134
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042001 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC=C([N+](=O)[O-])C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 61, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 89, 89, 89, 89, 61, 12, 1, 1, 1, 1, 1, 89] 89
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 19, 20, 23, 24, 25, 26, 27, 28])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042001 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042001
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `/scratch/stefan/7769623/finished'
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042001/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042001
Building REAL300000042002
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042002'
/scratch/stefan/7769623/working/building/REAL300000042002 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042002

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042002/0 /scratch/stefan/7769623/working/building/REAL300000042002 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/2
`/scratch/stefan/7769623/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCCCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042002 none CC(CC1CCCCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17] 24
rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 9, 42, 39, 44, 34, 8, 35, 43, 41, 36, 38, 10, 37] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042002 none CC(CC1CCCCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 4, 12, 16, 17, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 12, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1] 24
rigid atoms, others: [22, 23, 24, 18, 19, 20, 21, 54, 55, 56, 57, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042002 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042002
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042002/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042002
Building REAL300000042003
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042003'
/scratch/stefan/7769623/working/building/REAL300000042003 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042003

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042003/0 /scratch/stefan/7769623/working/building/REAL300000042003 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/3
`/scratch/stefan/7769623/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CN1C=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=N1)

`REAL300000042003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042003 none COC(=O)CN1C=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 52, 1, 1, 1, 1, 1, 7, 7, 34, 34, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 52, 52, 52, 8, 8, 1, 7, 7, 7, 7, 55, 55, 55, 55] 201
rigid atoms, others: [4, 5, 6, 7, 8, 21, 22, 28] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042003 none COC(=O)CN1C=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 55, 55, 55, 22, 6, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 201, 201, 201, 144, 144, 55, 22, 22, 22, 22, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 699
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042003 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042003
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042003/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042003
Building REAL300000042004
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042004'
/scratch/stefan/7769623/working/building/REAL300000042004 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042004

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042004/0 /scratch/stefan/7769623/working/building/REAL300000042004 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/4
`/scratch/stefan/7769623/working/3D/4' -> `0.mol2'
Preparing input files

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

`REAL300000042004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042004 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 40, 40, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 13, 40, 82, 82, 82, 1] 82
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042004 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 82, 81, 82, 82, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 81, 82, 82, 53, 8, 1, 1, 1, 82] 82
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042004 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042004
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042004/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042004
Building REAL300000042005
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042005'
/scratch/stefan/7769623/working/building/REAL300000042005 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042005

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042005/0 /scratch/stefan/7769623/working/building/REAL300000042005 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/5
`/scratch/stefan/7769623/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=C1)

`REAL300000042005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042005 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 95, 95, 95, 95, 95, 201, 201, 201, 201, 201, 95, 1, 1, 1, 1, 10, 45, 95, 95, 95, 201, 201, 201, 201, 95, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 303
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042005 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 164, 61, 61, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 164, 61, 13, 13, 13, 1, 1, 1, 1, 13, 201] 201
rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 489
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042005 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 95, 95, 95, 95, 45, 8, 1, 1, 1, 13, 13, 13, 13, 1, 95] 201
rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 16, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37])
total number of confs: 191
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042005 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042005
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042005/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042005
Building REAL300000042006
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042006'
/scratch/stefan/7769623/working/building/REAL300000042006 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042006

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042006/0 /scratch/stefan/7769623/working/building/REAL300000042006 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/6
`/scratch/stefan/7769623/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C=C2C(F)(F)F)=C1)

`REAL300000042006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042006 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 41, 41, 51, 51, 41, 41, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 13, 41, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042006 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 51, 51, 51, 51, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 51, 51, 51, 51, 30, 5, 1, 1, 1, 51] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042006 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042006
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042006/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042006
Building REAL300000042007
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042007'
/scratch/stefan/7769623/working/building/REAL300000042007 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042007

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042007/0 /scratch/stefan/7769623/working/building/REAL300000042007 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/7
`/scratch/stefan/7769623/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(Br)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042007 none COC1=C(Br)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 25, 41, 41, 41, 41, 41, 41, 41, 41, 1, 8, 8, 8, 1, 7, 25, 41, 41, 41, 41] 41
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 23] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042007 none COC1=C(Br)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 24, 8, 1, 1, 1, 1] 41
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042007 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042007
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042007/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042007
Building REAL300000042008
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042008'
/scratch/stefan/7769623/working/building/REAL300000042008 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042008

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042008/0 /scratch/stefan/7769623/working/building/REAL300000042008 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/8
`/scratch/stefan/7769623/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042008 none CC(CC1CCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 18, 18, 18, 8, 38, 38, 72, 72, 72, 72, 72, 72, 72, 72, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 72, 72, 72, 72] 135
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 172
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042008 none CC(CC1CCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [39, 8, 39, 55, 72, 72, 72, 72, 72, 109, 109, 135, 135, 135, 135, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 39, 39, 55, 55, 72, 72, 72, 72, 72, 72, 72, 135, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 1, 1] 135
rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 458
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042008 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042008
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042008/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042008
Building REAL300000042009
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042009'
/scratch/stefan/7769623/working/building/REAL300000042009 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042009

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042009/0 /scratch/stefan/7769623/working/building/REAL300000042009 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/9
`/scratch/stefan/7769623/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1[O-])

`REAL300000042009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042009 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 21, 21] 21
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 40
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042009 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042009 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042009/1 /scratch/stefan/7769623/working/building/REAL300000042009 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/10
`/scratch/stefan/7769623/working/3D/10' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1O)

`REAL300000042009.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042009/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042009 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 68, 68, 68, 67, 68, 68, 68, 68, 38, 38, 38, 10, 1, 1, 1, 1, 68, 68, 136] 136
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 262
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042009 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=C(F)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [11, 1, 11, 11, 42, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 42, 68, 68, 68, 68, 1, 1, 2] 136
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 155
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042009 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042009
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042009/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042009/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042009
Building REAL300000042010
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042010'
/scratch/stefan/7769623/working/building/REAL300000042010 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042010

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042010/0 /scratch/stefan/7769623/working/building/REAL300000042010 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/11
`/scratch/stefan/7769623/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(NC(C)=O)=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042010 none COC1=CC(NC(C)=O)=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 12, 12, 12, 67, 137, 137, 137, 137, 137, 137, 137, 137, 4, 4, 4, 1, 5, 5, 5, 5, 1, 1, 13, 13, 13, 67, 137, 137, 137, 137] 201
rigid atoms, others: [1, 2, 3, 4, 5, 33, 9, 10, 11, 12, 34, 28] set([0, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 290
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042010 none COC1=CC(NC(C)=O)=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 137, 137, 137, 95, 137, 201, 201, 201, 137, 137, 39, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 146, 146, 146, 137, 201, 201, 201, 201, 137, 137, 39, 39, 39, 10, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 602
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042010 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042010
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042010/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042010
Building REAL300000042011
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042011'
/scratch/stefan/7769623/working/building/REAL300000042011 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042011

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042011/0 /scratch/stefan/7769623/working/building/REAL300000042011 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/12
`/scratch/stefan/7769623/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1)

`REAL300000042011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042011 none CC(C)(C)C1CCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1] 15
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 9, 7, 44, 45, 46, 43, 20, 21, 36, 38, 37, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42])
total number of confs: 30
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042011 none CC(C)(C)C1CCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15] 15
rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 34
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042011 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042011
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042011/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042011
Building REAL300000042012
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042012'
/scratch/stefan/7769623/working/building/REAL300000042012 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042012

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042012/0 /scratch/stefan/7769623/working/building/REAL300000042012 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/13
`/scratch/stefan/7769623/working/3D/13' -> `0.mol2'
Preparing input files

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

`REAL300000042012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042012 none O=C([O-])C1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 41, 41, 95, 95, 95, 95, 95, 95, 41, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 13, 41, 95, 41, 95, 1] 95
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 25, 26, 27, 28] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042012 none O=C([O-])C1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 94, 95, 95, 62, 12, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 95, 94, 95, 95, 62, 12, 1, 1, 1, 95] 95
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 18, 19, 20, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042012 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042012
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042012/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042012
Building REAL300000042013
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042013'
/scratch/stefan/7769623/working/building/REAL300000042013 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042013

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042013/0 /scratch/stefan/7769623/working/building/REAL300000042013 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/14
`/scratch/stefan/7769623/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(Br)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042013 none COC1=CC=C(Br)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 3, 3, 3, 1, 1, 10, 38, 49, 49, 49, 49, 1] 71
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042013 none COC1=CC=C(Br)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 49, 49, 49, 49, 49, 49, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 71, 71, 71, 49, 49, 33, 11, 1, 1, 1, 1, 49] 71
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042013 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042013
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042013/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042013
Building REAL300000042014
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042014'
/scratch/stefan/7769623/working/building/REAL300000042014 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042014

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042014/0 /scratch/stefan/7769623/working/building/REAL300000042014 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/15
`/scratch/stefan/7769623/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C(F)C=C(F)C=C23)=C1)

`REAL300000042014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042014 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(F)C=C(F)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 28
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042014 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(F)C=C(F)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 26
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042014 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042014
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042014/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042014
Building REAL300000042015
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042015'
/scratch/stefan/7769623/working/building/REAL300000042015 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042015

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042015/0 /scratch/stefan/7769623/working/building/REAL300000042015 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/16
`/scratch/stefan/7769623/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C(F)C=CC(F)=C23)=C1)

`REAL300000042015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042015 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(F)C=CC(F)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042015 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(F)C=CC(F)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 20] 20
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042015 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042015
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042015/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042015
Building REAL300000042016
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042016'
/scratch/stefan/7769623/working/building/REAL300000042016 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042016

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042016/0 /scratch/stefan/7769623/working/building/REAL300000042016 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/17
`/scratch/stefan/7769623/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=C1)

`REAL300000042016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042016 none O=C([O-])C1=CC=CC(N=NC2CCCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 48, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 58
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042016 none O=C([O-])C1=CC=CC(N=NC2CCCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 27, 27, 27, 27, 15, 15, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 27, 27, 27, 27, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 27] 27
rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48])
total number of confs: 45
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042016 none O=C([O-])C1=CC=CC(N=NC2CCCCC(N3C(=O)C4=CC=CC=C4C3=O)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 27, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 27] 27
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 47, 46, 41, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 42, 43, 44, 45, 48])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042016 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042016
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042016/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042016
Building REAL300000042017
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042017'
/scratch/stefan/7769623/working/building/REAL300000042017 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042017

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042017/0 /scratch/stefan/7769623/working/building/REAL300000042017 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/18
`/scratch/stefan/7769623/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C(F)(F)C1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1)

`REAL300000042017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042017 none CCOC(=O)C(F)(F)C1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 32, 31, 5, 31, 1, 5, 5, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 38, 38, 38, 38, 1, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 39, 8, 9, 10, 11, 12, 40, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042017 none CCOC(=O)C(F)(F)C1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 190, 72, 190, 38, 72, 72, 38, 38, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 38, 38] 201
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 652
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042017 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042017
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042017/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042017
Building REAL300000042018
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042018'
/scratch/stefan/7769623/working/building/REAL300000042018 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042018

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042018/0 /scratch/stefan/7769623/working/building/REAL300000042018 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/19
`/scratch/stefan/7769623/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1C1=CC=CC=C1)

`REAL300000042018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042018 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 13, 13, 13, 13, 1, 1, 1, 2, 2, 1, 2, 2] 13
rigid atoms, others: [0, 1, 2, 3, 4, 34, 15, 16, 17, 35, 36, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 37, 38, 39, 40, 41])
total number of confs: 35
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: REAL300000042018 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1] 13
rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 21
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042018 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13] 13
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 27
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042018 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042018
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042018/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042018
Building REAL300000042019
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042019'
/scratch/stefan/7769623/working/building/REAL300000042019 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042019

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042019/0 /scratch/stefan/7769623/working/building/REAL300000042019 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/20
`/scratch/stefan/7769623/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(CC(N=NC2=CC=CC(C(=O)[O-])=C2)C2CC2)=C1)

`REAL300000042019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042019 none COC1=CC=CC(CC(N=NC2=CC=CC(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 4, 13, 67, 67, 158, 158, 158, 158, 158, 158, 158, 158, 13, 34, 34, 1, 3, 3, 3, 1, 1, 1, 4, 4, 13, 158, 158, 158, 158, 34, 34, 34, 34, 34, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 42, 23, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 315
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042019 none COC1=CC=CC(CC(N=NC2=CC=CC(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 34, 34, 34, 34, 17, 7, 1, 7, 27, 27, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 34, 49, 49, 49, 34, 34, 34, 17, 17, 7, 70, 70, 70, 70, 1, 1, 1, 1, 1, 34] 201
rigid atoms, others: [37, 38, 39, 8, 41, 40, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42])
total number of confs: 212
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042019 none COC1=CC=CC(CC(N=NC2=CC=CC(C(=O)[O-])=C2)C2CC2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [178, 158, 158, 158, 158, 158, 97, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 70, 70, 158, 178, 178, 178, 158, 158, 158, 97, 97, 43, 1, 1, 1, 1, 70, 70, 70, 70, 70, 158] 201
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 626
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042019 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042019
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042019/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042019
Building REAL300000042020
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042020'
/scratch/stefan/7769623/working/building/REAL300000042020 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042020

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042020/0 /scratch/stefan/7769623/working/building/REAL300000042020 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/21
`/scratch/stefan/7769623/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)O1)

`REAL300000042020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042020 none CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 28, 28, 56, 68, 68, 68, 68, 68, 68, 68, 68, 10, 1, 2, 2, 2, 1, 1, 10, 28, 56, 68, 68, 68, 68] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042020 none CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 40, 40, 40, 40, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 68, 68, 68, 68, 68, 68, 40, 23, 8, 1, 1, 1, 1] 68
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 113
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042020 none CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 7, 7, 26, 40, 40, 40, 40, 40, 40, 40, 40, 1, 10, 10, 10, 10, 10, 10, 1, 7, 26, 40, 40, 40, 40] 68
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042020 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042020
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042020/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042020
Building REAL300000042021
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042021'
/scratch/stefan/7769623/working/building/REAL300000042021 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042021

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042021/0 /scratch/stefan/7769623/working/building/REAL300000042021 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/22
`/scratch/stefan/7769623/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CO)C2=CC=C(F)C=C2F)=C1)

`REAL300000042021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042021 none O=C([O-])C1=CC=CC(NN=C(CO)C2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 74, 43, 84, 84, 46, 84, 84, 84, 84, 1, 1, 1, 1, 10, 74, 74, 222, 84, 84, 84, 1] 255
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 625
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042021 none O=C([O-])C1=CC=CC(NN=C(CO)C2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 84, 84, 84, 84, 40, 11, 11, 1, 11, 29, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 40, 29, 29, 87, 1, 1, 1, 84] 255
rigid atoms, others: [10, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 320
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042021 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042021
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042021/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042021
Building REAL300000042022
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042022'
/scratch/stefan/7769623/working/building/REAL300000042022 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042022

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042022/0 /scratch/stefan/7769623/working/building/REAL300000042022 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/23
`/scratch/stefan/7769623/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2CCCCO2)C(F)=C1)

`REAL300000042022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042022 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2CCCCO2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 36, 36, 36, 36, 97, 166, 201, 201, 201, 201, 201, 36, 36, 36, 10, 10, 10, 3, 1, 1, 1, 1, 36, 36, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 201, 36] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 575
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: REAL300000042022 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2CCCCO2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 172, 172, 200, 201, 201, 201, 201, 201, 201, 201, 201, 48, 64, 64, 28, 6, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 172, 172, 172, 200, 201, 201, 201, 201, 64, 64, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64] 201
rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49])
total number of confs: 561
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042022 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2CCCCO2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 12, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 23, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 10, 34, 64, 64, 64, 64, 64, 1, 1, 1, 9, 9, 9, 23, 36, 36, 36, 36, 1, 1, 34, 34, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1] 201
rigid atoms, others: [1, 36, 37, 49, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 281
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042022 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042022
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042022/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042022
Building REAL300000042023
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042023'
/scratch/stefan/7769623/working/building/REAL300000042023 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042023

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042023/0 /scratch/stefan/7769623/working/building/REAL300000042023 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/24
`/scratch/stefan/7769623/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CN=NC1=CC=CC(C(=O)[O-])=C1)C(C[N+](=O)[O-])C1=CC=CC=C1)

`REAL300000042023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042023 none CC(C)(CN=NC1=CC=CC(C(=O)[O-])=C1)C(C[N+](=O)[O-])C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 136, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 135, 197, 198, 201, 201, 200, 200, 200, 200, 200, 200, 145, 145, 145, 145, 145, 145, 44, 44, 1, 1, 1, 1, 194, 201, 201, 200, 200, 200, 200, 200] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 14, 37] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 954
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042023 none CC(C)(CN=NC1=CC=CC(C(=O)[O-])=C1)C(C[N+](=O)[O-])C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 2, 9, 9, 33, 126, 126, 200, 200, 200, 200, 200, 200, 200, 200, 1, 2, 4, 8, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 33, 33, 200, 200, 200, 200, 2, 4, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 15, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 394
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042023 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042023
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042023/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042023
Building REAL300000042024
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042024'
/scratch/stefan/7769623/working/building/REAL300000042024 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042024

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042024/0 /scratch/stefan/7769623/working/building/REAL300000042024 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/25
`/scratch/stefan/7769623/working/3D/25' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(Cl)=CC=C2N1)

`REAL300000042024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042024 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(Cl)=CC=C2N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 12, 12, 64, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 64, 94, 94, 94, 94, 1, 1, 1, 1] 94
rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042024 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(Cl)=CC=C2N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 42, 10, 1, 1, 1, 1, 94, 94, 94, 94] 94
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042024 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042024
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042024/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042024
Building REAL300000042025
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042025'
/scratch/stefan/7769623/working/building/REAL300000042025 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042025

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042025/0 /scratch/stefan/7769623/working/building/REAL300000042025 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/26
`/scratch/stefan/7769623/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2CCC(N=NC3=CC=CC(C(=O)[O-])=C3)CC2=C1)

`REAL300000042025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042025 none COC1=CC=C2CCC(N=NC3=CC=CC(C(=O)[O-])=C3)CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 1, 1, 1] 25
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39] set([0, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042025 none COC1=CC=C2CCC(N=NC3=CC=CC(C(=O)[O-])=C3)CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 25, 25, 25] 25
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 56
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042025 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042025
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042025/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042025
Building REAL300000042026
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042026'
/scratch/stefan/7769623/working/building/REAL300000042026 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042026

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042026/0 /scratch/stefan/7769623/working/building/REAL300000042026 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/27
`/scratch/stefan/7769623/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=C1)

`REAL300000042026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042026 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 54, 54, 68, 68, 63, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 13, 54, 68, 68, 68, 68, 68, 68, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042026 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 42, 15, 15, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 68, 68, 68, 68, 42, 15, 3, 3, 1, 1, 1, 1, 3, 68] 68
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 144
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042026 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=NC=C3)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 67, 68, 68, 31, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 68, 67, 68, 68, 31, 8, 1, 1, 3, 3, 3, 3, 1, 68] 68
rigid atoms, others: [36, 10, 11, 12, 13, 14, 15, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 37])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042026 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042026
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042026/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042026
Building REAL300000042027
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042027'
/scratch/stefan/7769623/working/building/REAL300000042027 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042027

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042027/0 /scratch/stefan/7769623/working/building/REAL300000042027 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/28
`/scratch/stefan/7769623/working/3D/28' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC(Cl)=CC(Cl)=C32)=C1)

`REAL300000042027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042027 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(Cl)=CC(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042027 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(Cl)=CC(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 10, 1, 1, 1, 1, 1, 1, 20] 20
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042027 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042027
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042027/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042027
Building REAL300000042028
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042028'
/scratch/stefan/7769623/working/building/REAL300000042028 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042028

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042028/0 /scratch/stefan/7769623/working/building/REAL300000042028 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/29
`/scratch/stefan/7769623/working/3D/29' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C([N+](=O)[O-])=C1)

`REAL300000042028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042028 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 47, 47, 40, 45, 47, 47, 47, 47, 47, 24, 24, 24, 5, 1, 1, 1, 1, 47, 47, 47] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 108
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042028 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [11, 1, 11, 11, 41, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 41, 47, 47, 47, 47, 1, 1, 1] 47
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 113
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042028 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042028
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042028/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042028
Building REAL300000042029
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042029'
/scratch/stefan/7769623/working/building/REAL300000042029 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042029

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042029/0 /scratch/stefan/7769623/working/building/REAL300000042029 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/30
`/scratch/stefan/7769623/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=C1)

`REAL300000042029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042029 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 89, 89, 89, 89, 197, 201, 201, 201, 201, 201, 89, 1, 1, 1, 1, 9, 46, 89, 89, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([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: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042029 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 176, 83, 83, 35, 35, 35, 35, 5, 1, 1, 1, 1, 1, 1, 1, 35, 201, 201, 201, 201, 176, 83, 35, 35, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 494
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042029 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 43, 7, 7, 1, 1, 1, 1, 1, 1, 13, 35, 35, 19, 35, 35, 1, 89, 89, 89, 89, 43, 7, 1, 1, 35, 35, 35, 35, 35, 89] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 272
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042029 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042029
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042029/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042029
Building REAL300000042030
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042030'
/scratch/stefan/7769623/working/building/REAL300000042030 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042030

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042030/0 /scratch/stefan/7769623/working/building/REAL300000042030 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/31
`/scratch/stefan/7769623/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1)

`REAL300000042030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042030 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 49, 49, 65, 65, 65, 93, 93, 93, 93, 93, 93, 93, 65, 65, 1, 1, 1, 1, 11, 49, 65, 93, 93, 93, 1] 93
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042030 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 67, 20, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 93, 93, 93, 93, 66, 19, 6, 1, 1, 1, 93] 93
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 215
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042030 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [65, 65, 65, 65, 65, 65, 65, 32, 6, 6, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 1, 1, 65, 65, 65, 65, 31, 6, 1, 6, 6, 6, 65] 93
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042030 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042030/1 /scratch/stefan/7769623/working/building/REAL300000042030 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/32
`/scratch/stefan/7769623/working/3D/32' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1)

`REAL300000042030.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042030/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042030 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 38, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 108, 1, 1, 1, 1, 37, 38, 108, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042030 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 149, 149, 37, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 37, 37, 7, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 357
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042030 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 16, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 55, 55, 9, 1, 1, 1, 1, 1, 7, 7, 2, 6, 7, 7, 7, 1, 1, 108, 108, 108, 108, 9, 9, 1, 7, 7, 7, 108] 201
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042030 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042030
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042030/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042030/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042030
Building REAL300000042031
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042031'
/scratch/stefan/7769623/working/building/REAL300000042031 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042031

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042031/0 /scratch/stefan/7769623/working/building/REAL300000042031 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/33
`/scratch/stefan/7769623/working/3D/33' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1)

`REAL300000042031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042031 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 49, 49, 67, 67, 67, 95, 95, 95, 95, 95, 95, 95, 67, 67, 1, 1, 1, 1, 11, 49, 67, 95, 95, 95, 1] 95
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042031 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 69, 19, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 95, 95, 95, 95, 68, 19, 6, 1, 1, 1, 95] 95
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 218
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042031 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [67, 67, 67, 67, 67, 67, 67, 34, 6, 6, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 6, 1, 1, 67, 67, 67, 67, 33, 6, 1, 6, 6, 6, 67] 95
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042031 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042031/1 /scratch/stefan/7769623/working/building/REAL300000042031 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/34
`/scratch/stefan/7769623/working/3D/34' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1)

`REAL300000042031.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042031/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042031 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 38, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 108, 1, 1, 1, 1, 37, 38, 108, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042031 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 149, 149, 37, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 37, 37, 7, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 357
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042031 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C(Cl)=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 55, 55, 9, 1, 1, 1, 1, 1, 7, 7, 6, 6, 7, 7, 7, 1, 1, 108, 108, 108, 108, 9, 9, 1, 7, 7, 7, 108] 201
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 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
/scratch/stefan/7769623/working/building/REAL300000042031 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042031
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042031/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042031/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042031
Building REAL300000042032
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042032'
/scratch/stefan/7769623/working/building/REAL300000042032 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042032

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042032/0 /scratch/stefan/7769623/working/building/REAL300000042032 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/35
`/scratch/stefan/7769623/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CCC(CN=NC2=CC=CC(C(=O)[O-])=C2)CC1)

`REAL300000042032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042032 none CC(C)(C)C1CCC(CN=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 42, 42, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 79, 79, 79, 79, 1, 1, 1, 1] 79
rigid atoms, others: [32, 1, 34, 35, 4, 5, 6, 33, 8, 7, 44, 45, 46, 43, 20, 21, 36, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42])
total number of confs: 135
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042032 none CC(C)(C)C1CCC(CN=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 79, 74, 79, 79, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 48, 48, 1, 1, 1, 1, 79, 79, 79, 79] 79
rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 299
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042032 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042032
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042032/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042032
Building REAL300000042033
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042033'
/scratch/stefan/7769623/working/building/REAL300000042033 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042033

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042033/0 /scratch/stefan/7769623/working/building/REAL300000042033 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/36
`/scratch/stefan/7769623/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=C1)

`REAL300000042033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042033 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 53, 53, 70, 70, 53, 70, 117, 134, 134, 134, 134, 134, 134, 70, 70, 70, 1, 1, 1, 1, 11, 53, 70, 70, 134, 134, 134, 134, 134, 134, 134, 70, 140, 1] 268
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 507
number of broken/clashed sets: 125
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042033 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [134, 134, 134, 134, 134, 134, 134, 91, 36, 36, 19, 19, 19, 19, 11, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 134, 134, 134, 134, 91, 36, 19, 19, 3, 3, 1, 1, 1, 1, 1, 19, 38, 134] 268
rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 338
number of broken/clashed sets: 125
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042033 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 25, 4, 4, 1, 1, 1, 1, 1, 1, 2, 10, 19, 19, 10, 19, 19, 1, 1, 1, 70, 70, 70, 70, 25, 4, 1, 1, 10, 10, 19, 19, 19, 19, 19, 1, 2, 70] 268
rigid atoms, others: [32, 33, 41, 10, 11, 12, 13, 14, 15, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 194
number of broken/clashed sets: 125
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042033 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042033
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042033/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042033
Building REAL300000042034
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042034'
/scratch/stefan/7769623/working/building/REAL300000042034 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042034

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042034/0 /scratch/stefan/7769623/working/building/REAL300000042034 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/37
`/scratch/stefan/7769623/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2Cl)=C1)

`REAL300000042034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042034 none O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 39, 39, 46, 46, 41, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 13, 39, 46, 46, 46, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042034 none O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 35, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 46, 46, 46, 46, 35, 8, 1, 1, 1, 46] 46
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042034 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042034
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042034/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042034
Building REAL300000042035
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042035'
/scratch/stefan/7769623/working/building/REAL300000042035 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042035

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042035/0 /scratch/stefan/7769623/working/building/REAL300000042035 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/38
`/scratch/stefan/7769623/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2CCCCC2)=N1)

`REAL300000042035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042035 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2CCCCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 47, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 6, 6, 6, 6, 6, 1, 2, 2, 2, 1, 10, 47, 82, 82, 82, 82, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 101
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 188
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: REAL300000042035 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2CCCCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 35, 35, 89, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 35, 89, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 101
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 251
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042035 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2CCCCC2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 82, 101, 101, 101, 101, 101, 82, 82, 82, 82, 82, 32, 6, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101] 101
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 198
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042035 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042035
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042035/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042035
Building REAL300000042036
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042036'
/scratch/stefan/7769623/working/building/REAL300000042036 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042036

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042036/0 /scratch/stefan/7769623/working/building/REAL300000042036 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/39
`/scratch/stefan/7769623/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1=NC(C)=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042036 none COCCC1=NC(C)=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 12, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 97, 97, 97, 97, 97, 97, 97, 97, 1, 33, 33, 33, 12, 12, 8, 8, 2, 2, 2, 9, 9, 9, 43, 97, 97, 97, 97] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 271
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042036 none COCCC1=NC(C)=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 97, 97, 97, 97, 97, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 97, 201, 201, 201, 201, 201, 177, 177, 97, 97, 97, 26, 26, 26, 6, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 666
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042036 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042036
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042036/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042036
Building REAL300000042037
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042037'
/scratch/stefan/7769623/working/building/REAL300000042037 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042037

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042037/0 /scratch/stefan/7769623/working/building/REAL300000042037 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/40
`/scratch/stefan/7769623/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2C(F)(F)F)=C1)

`REAL300000042037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042037 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 47, 27, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 26
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042037 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 7, 7, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 12] 12
rigid atoms, others: [43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47])
total number of confs: 27
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042037 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 12] 12
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 43, 44, 45, 46, 47])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042037 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042037
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042037/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042037
Building REAL300000042038
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042038'
/scratch/stefan/7769623/working/building/REAL300000042038 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042038

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042038/0 /scratch/stefan/7769623/working/building/REAL300000042038 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/41
`/scratch/stefan/7769623/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Cl)

`REAL300000042038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042038 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 64, 64, 45, 64, 64, 64, 64, 64, 64, 46, 46, 46, 12, 1, 1, 1, 1, 64, 64, 64] 64
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 199
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042038 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 35, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 35, 64, 64, 64, 64, 1, 1, 1] 64
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 135
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042038 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042038
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042038/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042038
Building REAL300000042039
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042039'
/scratch/stefan/7769623/working/building/REAL300000042039 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042039

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042039/0 /scratch/stefan/7769623/working/building/REAL300000042039 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/42
`/scratch/stefan/7769623/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1)

`REAL300000042039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042039 none O=C([O-])C1=CC=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 40, 40, 40, 40, 77, 77, 77, 77, 77, 77, 77, 77, 77, 40, 1, 1, 1, 1, 11, 37, 40, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 40, 1] 77
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 49, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042039 none O=C([O-])C1=CC=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 47, 19, 19, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 77, 77, 77, 77, 47, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 77] 77
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 48, 49])
total number of confs: 156
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042039 none O=C([O-])C1=CC=CC(NN=CC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 40, 40, 40, 40, 16, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 40, 40, 40, 40, 16, 6, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 40] 77
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 48, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49])
total number of confs: 74
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042039 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042039/1 /scratch/stefan/7769623/working/building/REAL300000042039 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/43
`/scratch/stefan/7769623/working/3D/43' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1)

`REAL300000042039.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042039/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042039 none O=C([O-])C1=CC=CC(N=NCC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 109, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 1, 1, 1, 1, 35, 34, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 49, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042039 none O=C([O-])C1=CC=CC(N=NCC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 133, 133, 31, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 201, 201, 201, 201, 31, 31, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 201] 201
rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 48, 49])
total number of confs: 359
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042039 none O=C([O-])C1=CC=CC(N=NCC2=NNC(C34CC5CC(CC(C5)C3)C4)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 59, 59, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 109, 109, 109, 109, 9, 9, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 109] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 48, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042039 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042039
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042039/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042039/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042039
Building REAL300000042040
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042040'
/scratch/stefan/7769623/working/building/REAL300000042040 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042040

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042040/0 /scratch/stefan/7769623/working/building/REAL300000042040 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/44
`/scratch/stefan/7769623/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)SC1=CC(Br)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042040 none CC(C)SC1=CC(Br)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [23, 10, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 84, 84, 84, 84, 84, 84, 84, 84, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 9, 43, 84, 84, 84, 84] 148
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 231
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042040 none CC(C)SC1=CC(Br)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 146, 148, 84, 84, 84, 44, 84, 84, 84, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 148, 148, 148, 148, 148, 148, 148, 84, 84, 84, 32, 6, 1, 1, 1, 1] 148
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 379
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042040 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042040
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042040/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042040
Building REAL300000042041
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042041'
/scratch/stefan/7769623/working/building/REAL300000042041 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042041

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042041/0 /scratch/stefan/7769623/working/building/REAL300000042041 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/45
`/scratch/stefan/7769623/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)NC1=CC=NC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042041 none CC(C)(C)C(=O)NC1=CC=NC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 43, 69, 69, 69, 69, 69, 69, 69, 69, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 12, 43, 69, 69, 69, 69] 83
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042041 none CC(C)(C)C(=O)NC1=CC=NC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 83, 83, 69, 69, 69, 69, 69, 69, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 69, 69, 69, 34, 9, 1, 1, 1, 1] 83
rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 163
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042041 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042041
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042041/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042041
Building REAL300000042042
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042042'
/scratch/stefan/7769623/working/building/REAL300000042042 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042042

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042042/0 /scratch/stefan/7769623/working/building/REAL300000042042 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/46
`/scratch/stefan/7769623/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1)

`REAL300000042042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042042 none COC1=CC=C(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 12, 12, 63, 63, 152, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 1, 1, 2, 2, 2, 1, 1, 19, 19, 63, 152, 201, 201, 201, 201, 19, 19, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 43, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 513
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042042 none COC1=CC=C(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 183, 201, 201, 167, 41, 41, 70, 70, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 201, 201, 201, 201, 201, 201, 201, 70, 70, 24, 6, 1, 1, 1, 1, 70, 70, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 511
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042042 none COC1=CC=C(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 8, 8, 19, 19, 5, 1, 1, 1, 1, 1, 1, 6, 6, 34, 70, 70, 70, 70, 70, 71, 71, 70, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 6, 34, 70, 70, 70, 70, 1, 1, 19, 19] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 40, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42, 43])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042042 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042042
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042042/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042042
Building REAL300000042043
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042043'
/scratch/stefan/7769623/working/building/REAL300000042043 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042043

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042043/0 /scratch/stefan/7769623/working/building/REAL300000042043 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/47
`/scratch/stefan/7769623/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC(Br)=C1)

`REAL300000042043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042043 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 174, 174, 174, 170, 174, 174, 174, 86, 86, 86, 86, 86, 8, 1, 1, 1, 1, 174, 174, 174] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 473
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042043 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 12, 12, 83, 174, 174, 174, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 83, 174, 174, 174, 174, 1, 1, 1] 201
rigid atoms, others: [32, 33, 2, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 440
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042043 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042043
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042043/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042043
Building REAL300000042044
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042044'
/scratch/stefan/7769623/working/building/REAL300000042044 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042044

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042044/0 /scratch/stefan/7769623/working/building/REAL300000042044 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/48
`/scratch/stefan/7769623/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C(Br)=C2)=C1)

`REAL300000042044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042044 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 44, 44, 70, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 13, 44, 71, 71, 71, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042044 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 51, 9, 1, 1, 1, 71] 71
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042044 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042044
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042044/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042044
Building REAL300000042045
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042045'
/scratch/stefan/7769623/working/building/REAL300000042045 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042045

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042045/0 /scratch/stefan/7769623/working/building/REAL300000042045 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/49
`/scratch/stefan/7769623/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=C1)

`REAL300000042045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042045 none O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 26, 26, 26, 26, 26, 26, 23, 23, 1, 1, 1, 1, 23, 23, 23, 23, 26, 26, 26, 26, 23, 23, 23, 23, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042045 none O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 20, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 26] 26
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 37
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042045 none O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(F)C=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 2, 4, 5, 5, 1, 1, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 23] 26
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 31, 32, 33, 34, 39])
total number of confs: 48
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042045 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042045
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042045/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042045
Building REAL300000042046
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042046'
/scratch/stefan/7769623/working/building/REAL300000042046 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042046

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042046/0 /scratch/stefan/7769623/working/building/REAL300000042046 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/50
`/scratch/stefan/7769623/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1)

`REAL300000042046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042046 none COC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 9, 41, 123, 123, 123, 123, 1] 123
rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 216
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042046 none COC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 104, 104, 123, 123, 59, 59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 123, 123, 123, 123, 123, 123, 123, 123, 60, 60, 60, 12, 1, 1, 1, 1, 123] 123
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 283
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042046 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042046
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042046/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042046
Building REAL300000042047
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042047'
/scratch/stefan/7769623/working/building/REAL300000042047 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042047

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042047/0 /scratch/stefan/7769623/working/building/REAL300000042047 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/51
`/scratch/stefan/7769623/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C3=CC=CN=C23)=C1)

`REAL300000042047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042047 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C3=CC=CN=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 11, 25, 27, 27, 27, 27, 27, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042047 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C3=CC=CN=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 27, 27, 27, 27, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 20, 4, 1, 1, 1, 1, 1, 27] 27
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042047 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042047
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042047/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042047
Building REAL300000042048
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042048'
/scratch/stefan/7769623/working/building/REAL300000042048 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042048

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042048/0 /scratch/stefan/7769623/working/building/REAL300000042048 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/52
`/scratch/stefan/7769623/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C(C)N1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042048 none COC(=O)C(C)N1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 58, 99, 99, 99, 99, 99, 100, 100, 99, 17, 17, 17, 7, 8, 8, 8, 1, 1, 1, 10, 58, 99, 99, 99, 99] 201
rigid atoms, others: [32, 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, 33, 34, 35, 36, 37, 38])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042048 none COC(=O)C(C)N1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 147, 201, 99, 147, 99, 99, 99, 99, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 147, 148, 148, 148, 99, 99, 99, 32, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 615
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042048 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042048
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042048/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042048
Building REAL300000042049
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042049'
/scratch/stefan/7769623/working/building/REAL300000042049 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042049

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042049/0 /scratch/stefan/7769623/working/building/REAL300000042049 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/53
`/scratch/stefan/7769623/working/3D/53' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2F)=C1)

`REAL300000042049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042049 none O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 13, 33, 44, 44, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042049 none O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 43, 44, 44, 32, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 44, 43, 44, 44, 32, 8, 1, 1, 1, 44] 44
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 106
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042049 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042049
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042049/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042049
Building REAL300000042050
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042050'
/scratch/stefan/7769623/working/building/REAL300000042050 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042050

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042050/0 /scratch/stefan/7769623/working/building/REAL300000042050 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/54
`/scratch/stefan/7769623/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1)

`REAL300000042050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042050 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 20, 43, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 1, 42, 42, 42, 42, 1, 1, 1, 20, 20, 43, 43, 43, 43, 43] 201
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 15, 16, 17, 36, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042050 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 43, 43, 43, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 43, 18, 4, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 201, 201, 201, 201, 43, 43, 43, 4, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 346
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042050 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OCC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 100, 201, 201, 201, 201, 201, 201, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 42, 42, 42, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 672
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042050 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042050
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042050/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042050
Building REAL300000042051
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042051'
/scratch/stefan/7769623/working/building/REAL300000042051 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042051

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042051/0 /scratch/stefan/7769623/working/building/REAL300000042051 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/55
`/scratch/stefan/7769623/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042051 none CC(C)(C)OC(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 29, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 8, 8, 42, 89, 89, 89, 89, 89, 89, 89, 89, 1, 34, 34, 34, 33, 33, 33, 34, 34, 34, 1, 1, 1, 8, 42, 89, 89, 89, 89, 1] 201
rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 43, 24] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042051 none CC(C)(C)OC(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 167, 89, 167, 89, 88, 89, 89, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 89, 89, 36, 8, 1, 1, 1, 1, 89] 201
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 426
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042051 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042051
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042051/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042051
Building REAL300000042052
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042052'
/scratch/stefan/7769623/working/building/REAL300000042052 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042052

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042052/0 /scratch/stefan/7769623/working/building/REAL300000042052 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/56
`/scratch/stefan/7769623/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1[N+](=O)[O-])

`REAL300000042052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042052 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 49, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 2, 2, 4, 4, 4, 1, 11, 49, 121, 121, 121, 121, 1, 1] 121
rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042052 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 121, 58, 58, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 121, 121, 120, 120, 121, 121, 121, 121, 121, 121, 58, 12, 1, 1, 1, 1, 121, 121] 121
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 200
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042052 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042052
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042052/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042052
Building REAL300000042053
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042053'
/scratch/stefan/7769623/working/building/REAL300000042053 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042053

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042053/0 /scratch/stefan/7769623/working/building/REAL300000042053 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/57
`/scratch/stefan/7769623/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1OC(F)F)

`REAL300000042053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042053 none CC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 4, 28, 28, 2, 2, 2, 1, 1, 1, 6, 26, 71, 71, 71, 71, 28] 127
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042053 none CC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [71, 71, 40, 71, 71, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 97, 127, 127, 71, 71, 71, 71, 71, 71, 39, 10, 1, 1, 1, 1, 127] 127
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 464
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042053 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042053
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042053/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042053
Building REAL300000042054
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042054'
/scratch/stefan/7769623/working/building/REAL300000042054 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042054

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042054/0 /scratch/stefan/7769623/working/building/REAL300000042054 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/58
`/scratch/stefan/7769623/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(F)F)

`REAL300000042054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042054 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 16, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 2, 2, 1, 1, 1, 7, 37, 69, 69, 4, 4, 4, 1, 5, 16, 33, 33, 33, 33, 1, 37, 37, 69] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 17, 18, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 39, 40, 41])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042054 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 33, 33, 33, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 33, 33, 33, 33, 33, 117, 188, 201, 201, 65, 65, 65, 33, 21, 7, 1, 1, 1, 1, 33, 188, 188, 201] 201
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 659
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042054 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042054
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042054/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042054
Building REAL300000042055
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042055'
/scratch/stefan/7769623/working/building/REAL300000042055 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042055

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042055/0 /scratch/stefan/7769623/working/building/REAL300000042055 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/59
`/scratch/stefan/7769623/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC3=CC(Br)=CC=C3C=C2)=C1)

`REAL300000042055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042055 none O=C([O-])C1=CC=CC(NN=CC2=NC3=CC(Br)=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 28, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 11, 28, 34, 34, 34, 34, 34, 1] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 60
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042055 none O=C([O-])C1=CC=CC(NN=CC2=NC3=CC(Br)=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 21, 8, 1, 1, 1, 1, 1, 34] 34
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042055 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042055
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042055/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042055
Building REAL300000042056
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042056'
/scratch/stefan/7769623/working/building/REAL300000042056 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042056

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042056/0 /scratch/stefan/7769623/working/building/REAL300000042056 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/60
`/scratch/stefan/7769623/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1)

`REAL300000042056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042056 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 56, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 6, 6, 2, 6, 6, 1, 2, 2, 2, 1, 12, 56, 141, 141, 141, 141, 6, 6, 5, 6, 6] 154
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 276
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: REAL300000042056 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 30, 30, 107, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 30, 107, 154, 154, 154, 154, 1, 1, 1, 1, 1] 154
rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 335
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042056 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 70, 70, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 141, 141, 154, 154, 154, 154, 154, 141, 141, 141, 141, 141, 70, 13, 1, 1, 1, 1, 154, 154, 154, 154, 154] 154
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 234
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042056 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042056
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042056/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042056
Building REAL300000042057
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042057'
/scratch/stefan/7769623/working/building/REAL300000042057 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042057

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042057/0 /scratch/stefan/7769623/working/building/REAL300000042057 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/61
`/scratch/stefan/7769623/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042057 none CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 16, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 1, 1] 53
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 47, 48, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 102
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: REAL300000042057 none CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 52, 53, 21, 21, 35, 35, 21, 21, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 53, 53, 53, 53, 53, 53, 53, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 35, 35] 53
rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 170
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042057 none CC(C)OC1=CC=C(C2CCCC2N=NC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [22, 9, 22, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 22, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 3, 3] 53
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 35, 41, 36, 42, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48])
total number of confs: 106
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042057 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042057
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042057/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042057
Building REAL300000042058
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042058'
/scratch/stefan/7769623/working/building/REAL300000042058 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042058

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042058/0 /scratch/stefan/7769623/working/building/REAL300000042058 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/62
`/scratch/stefan/7769623/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=C1)

`REAL300000042058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042058 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 30
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: REAL300000042058 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 14] 14
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 29
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042058 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(C(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14] 14
rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41])
total number of confs: 34
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042058 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042058
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042058/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042058
Building REAL300000042059
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042059'
/scratch/stefan/7769623/working/building/REAL300000042059 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042059

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042059/0 /scratch/stefan/7769623/working/building/REAL300000042059 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/63
`/scratch/stefan/7769623/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C(Br)C=CC=C23)=C1)

`REAL300000042059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042059 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(Br)C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 25
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042059 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(Br)C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24])
total number of confs: 23
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042059 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042059
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042059/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042059
Building REAL300000042060
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042060'
/scratch/stefan/7769623/working/building/REAL300000042060 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042060

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042060/0 /scratch/stefan/7769623/working/building/REAL300000042060 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/64
`/scratch/stefan/7769623/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2OC(F)F)=C1)

`REAL300000042060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042060 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2OC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 11, 41, 41, 69, 69, 69, 69, 69, 69, 69, 102, 138, 138, 1, 1, 1, 1, 11, 41, 69, 69, 69, 138, 1] 138
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 393
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042060 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2OC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 12, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [69, 69, 69, 69, 69, 69, 69, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 22, 22, 69, 69, 69, 69, 27, 6, 1, 1, 1, 22, 69] 138
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042060 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042060
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042060/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042060
Building REAL300000042061
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042061'
/scratch/stefan/7769623/working/building/REAL300000042061 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042061

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042061/0 /scratch/stefan/7769623/working/building/REAL300000042061 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/65
`/scratch/stefan/7769623/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+]1CCN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)CC1)

`REAL300000042061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042061 none C[NH+]1CCN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 17, 17, 56, 63, 63, 63, 63, 63, 63, 63, 63, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 17, 56, 63, 63, 63, 63, 6, 6, 1, 1, 1, 1] 63
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 43, 44, 45, 46, 24, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 162
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: REAL300000042061 none C[NH+]1CCN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 51, 50, 52, 52, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 52, 63, 63, 63, 63, 63, 63, 63, 63, 63, 52, 52, 32, 10, 1, 1, 1, 1, 52, 52, 63, 63, 63, 63] 63
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 122
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042061 none C[NH+]1CCN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 9, 9, 43, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 9, 43, 52, 52, 52, 52, 1, 1, 6, 6, 6, 6] 63
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 121
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042061 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042061
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042061/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042061
Building REAL300000042062
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042062'
/scratch/stefan/7769623/working/building/REAL300000042062 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042062

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042062/0 /scratch/stefan/7769623/working/building/REAL300000042062 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/66
`/scratch/stefan/7769623/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC=C1OC)

`REAL300000042062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042062 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [89, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 125, 125, 125, 125, 125, 125, 125, 137, 89, 89, 89, 89, 89, 10, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 137, 137, 137] 146
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 415
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042062 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [31, 11, 1, 11, 11, 55, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 1, 3, 31, 31, 31, 31, 31, 55, 125, 125, 125, 125, 1, 2, 2, 2, 1, 1, 3, 3, 3] 146
rigid atoms, others: [33, 2, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 39, 40, 41])
total number of confs: 328
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042062 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042062
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042062/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042062
Building REAL300000042063
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042063'
/scratch/stefan/7769623/working/building/REAL300000042063 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042063

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042063/0 /scratch/stefan/7769623/working/building/REAL300000042063 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/67
`/scratch/stefan/7769623/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2NC3=C(CC(N=NC4=CC=CC(C(=O)[O-])=C4)CC3)C2=C1)

`REAL300000042063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042063 none CC1=CC=C2NC3=C(CC(N=NC4=CC=CC(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42] set([34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042063 none CC1=CC=C2NC3=C(CC(N=NC4=CC=CC(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15, 15] 15
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42])
total number of confs: 36
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042063 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042063
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042063/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042063
Building REAL300000042064
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042064'
/scratch/stefan/7769623/working/building/REAL300000042064 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042064

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042064/0 /scratch/stefan/7769623/working/building/REAL300000042064 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/68
`/scratch/stefan/7769623/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1)

`REAL300000042064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042064 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 69, 190, 190, 190, 190, 190, 190, 190, 190, 1, 1, 6, 6, 1, 1, 1, 6, 6, 1, 2, 2, 2, 1, 11, 69, 190, 190, 190, 190, 6, 6, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 345
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: REAL300000042064 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 30, 30, 132, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 30, 132, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 429
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042064 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(C#N)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 190, 190, 79, 79, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 190, 190, 201, 201, 190, 190, 190, 201, 201, 190, 190, 190, 190, 190, 79, 13, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 327
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042064 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042064
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042064/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042064
Building REAL300000042065
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042065'
/scratch/stefan/7769623/working/building/REAL300000042065 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042065

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042065/0 /scratch/stefan/7769623/working/building/REAL300000042065 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/69
`/scratch/stefan/7769623/working/3D/69' -> `0.mol2'
Preparing input files

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

`REAL300000042065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042065 none CC(CC1=CC=C(Cl)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 85, 85, 85, 85, 85, 85, 85, 85, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 85, 85, 85, 85] 85
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042065 none CC(CC1=CC=C(Cl)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 8, 44, 81, 85, 85, 85, 85, 85, 85, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 44, 81, 81, 85, 85, 85, 85, 1, 1, 1, 1] 85
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 330
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042065 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042065
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042065/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042065
Building REAL300000042066
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042066'
/scratch/stefan/7769623/working/building/REAL300000042066 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042066

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042066/0 /scratch/stefan/7769623/working/building/REAL300000042066 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/70
`/scratch/stefan/7769623/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CCCC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042066 none CC(C)(C)OC(=O)NC1CCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 31, 34, 34, 12, 7, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 52, 52, 52, 52, 52, 52, 52, 52, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45])
total number of confs: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042066 none CC(C)(C)OC(=O)NC1CCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 175, 129, 175, 52, 52, 52, 52, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 575
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042066 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042066
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042066/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042066
Building REAL300000042067
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042067'
/scratch/stefan/7769623/working/building/REAL300000042067 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042067

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042067/0 /scratch/stefan/7769623/working/building/REAL300000042067 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/71
`/scratch/stefan/7769623/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042067 none CS(=O)(=O)C1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 1, 1, 1, 6, 25, 47, 47, 47, 47] 47
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042067 none CS(=O)(=O)C1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 42, 47, 47, 47, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 47, 47, 43, 47, 31, 9, 1, 1, 1, 1] 47
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042067 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042067
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042067/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042067
Building REAL300000042068
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042068'
/scratch/stefan/7769623/working/building/REAL300000042068 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042068

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042068/0 /scratch/stefan/7769623/working/building/REAL300000042068 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/72
`/scratch/stefan/7769623/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1OC(F)F)

`REAL300000042068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042068 none CC1=CC(Br)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 26, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 4, 24, 24, 2, 2, 2, 1, 1, 4, 26, 71, 71, 71, 71, 24] 142
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042068 none CC1=CC(Br)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [71, 71, 40, 71, 71, 71, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 104, 142, 142, 71, 71, 71, 71, 71, 38, 10, 1, 1, 1, 1, 142] 142
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 537
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042068 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042068
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042068/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042068
Building REAL300000042069
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042069'
/scratch/stefan/7769623/working/building/REAL300000042069 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042069

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042069/0 /scratch/stefan/7769623/working/building/REAL300000042069 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/73
`/scratch/stefan/7769623/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=C1)

`REAL300000042069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042069 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 55
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: REAL300000042069 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 18, 18, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 26] 26
rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 41
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042069 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 4, 5, 5, 5, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19] 26
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38])
total number of confs: 41
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042069 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042069
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042069/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042069
Building REAL300000042070
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042070'
/scratch/stefan/7769623/working/building/REAL300000042070 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042070

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042070/0 /scratch/stefan/7769623/working/building/REAL300000042070 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/74
`/scratch/stefan/7769623/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042070 none COC(=O)CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 8, 45, 1, 1, 1, 1, 1, 1, 1, 8, 8, 38, 64, 64, 64, 64, 64, 65, 65, 64, 45, 45, 45, 8, 8, 1, 1, 1, 8, 38, 64, 64, 64, 64] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 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: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042070 none COC(=O)CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 142, 201, 64, 64, 64, 64, 64, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 142, 142, 64, 64, 64, 23, 5, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 687
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042070 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042070
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042070/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042070
Building REAL300000042071
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042071'
/scratch/stefan/7769623/working/building/REAL300000042071 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042071

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042071/0 /scratch/stefan/7769623/working/building/REAL300000042071 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/75
`/scratch/stefan/7769623/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=C1)

`REAL300000042071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042071 none O=C([O-])C1=CC=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 41, 141, 201, 201, 201, 41, 78, 78, 61, 78, 78, 1, 1, 1, 1, 9, 141, 141, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 856
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: REAL300000042071 none O=C([O-])C1=CC=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 21, 4, 4, 1, 4, 29, 64, 64, 64, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 21, 29, 29, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 78] 201
rigid atoms, others: [36, 37, 38, 39, 40, 10, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 317
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042071 none O=C([O-])C1=CC=CC(NN=C(CC2CCC2)C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 118, 42, 42, 7, 1, 1, 1, 1, 1, 42, 64, 64, 55, 64, 64, 201, 201, 201, 201, 118, 7, 7, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 201] 201
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41])
total number of confs: 530
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042071 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042071
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042071/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042071
Building REAL300000042072
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042072'
/scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000042072

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042072/0 /scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/76
`/scratch/stefan/7769623/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 12, 14, 14, 1, 1, 1, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 1, 1, 10, 10, 14, 14, 13, 14, 14, 1, 1, 1, 27, 27, 27, 27] 56
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 41, 42, 43, 13, 14, 15, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47])
total number of confs: 87
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: REAL300000042072 none CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [27, 27, 27, 27, 27, 27, 27, 56, 56, 56, 56, 56, 56, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 56, 56, 56, 56, 56, 56, 56, 27, 27, 27, 1, 1, 1, 1] 56
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 197
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CC[N@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 14, 14, 3, 14, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 42, 42, 56, 56, 56, 56, 56, 56, 56, 56, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 56, 56, 56, 56] 56
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 103
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042072/1 /scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/77
`/scratch/stefan/7769623/working/3D/77' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042072.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042072/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 8, 12, 12, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 1, 1, 1, 1, 1, 8, 8, 12, 12, 8, 12, 12, 1, 1, 1, 34, 34, 34, 34] 68
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 41, 42, 43, 13, 14, 15, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47])
total number of confs: 93
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: REAL300000042072 none CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [34, 34, 34, 34, 34, 34, 34, 68, 68, 68, 68, 68, 68, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 68, 68, 68, 68, 68, 68, 68, 34, 34, 34, 1, 1, 1, 1] 68
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 232
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CC[N@@H+](CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [12, 12, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 48, 48, 68, 68, 68, 68, 68, 68, 68, 68, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 12, 12, 12, 68, 68, 68, 68] 68
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 117
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `2'
/scratch/stefan/7769623/working/building/REAL300000042072/2 /scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 2 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/78
`/scratch/stefan/7769623/working/3D/78' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042072.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000042072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042072/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 14, 14, 12, 14, 14, 1, 1, 1, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1, 1, 33, 33, 33, 33] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 40, 41, 42, 12, 13, 14, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 70, 70, 70, 70, 70, 70, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 33, 33, 33, 33, 33, 33, 70, 70, 70, 70, 70, 70, 70, 33, 33, 33, 1, 1, 1, 1] 70
rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 241
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042072 none CC1CCN(CC2=CC=CC=C2)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 38, 38, 70, 70, 70, 70, 70, 70, 70, 70, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 14, 14, 14, 70, 70, 70, 70] 70
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042072 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042072
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
2: /scratch/stefan/7769623/working/building/REAL300000042072/2.*
0: /scratch/stefan/7769623/working/building/REAL300000042072/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042072/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042072
Building REAL300000042073
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042073'
/scratch/stefan/7769623/working/building/REAL300000042073 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042073

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042073/0 /scratch/stefan/7769623/working/building/REAL300000042073 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/79
`/scratch/stefan/7769623/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(O)C3=CC=CC=C3C(Cl)=C2)=C1)

`REAL300000042073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042073 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C3=CC=CC=C3C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 9, 31, 66, 33, 33, 33, 33, 33, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 117
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042073 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C3=CC=CC=C3C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 28, 8, 2, 1, 1, 1, 1, 1, 33] 66
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 75
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042073 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042073/1 /scratch/stefan/7769623/working/building/REAL300000042073 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/80
`/scratch/stefan/7769623/working/3D/80' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C([O-])C3=CC=CC=C3C(Cl)=C2)=C1)

`REAL300000042073.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042073/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042073 none O=C([O-])C1=CC=CC(NN=CC2=C([O-])C3=CC=CC=C3C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 24
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042073 none O=C([O-])C1=CC=CC(NN=CC2=C([O-])C3=CC=CC=C3C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 10, 4, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 23, 24, 25, 26, 27, 28])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042073 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042073
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042073/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042073/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042073
Building REAL300000042074
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042074'
/scratch/stefan/7769623/working/building/REAL300000042074 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042074

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042074/0 /scratch/stefan/7769623/working/building/REAL300000042074 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/81
`/scratch/stefan/7769623/working/3D/81' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(Cl)C=C32)=C1)

`REAL300000042074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042074 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 28
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042074 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24])
total number of confs: 26
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042074 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042074
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042074/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042074
Building REAL300000042075
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042075'
/scratch/stefan/7769623/working/building/REAL300000042075 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042075

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042075/0 /scratch/stefan/7769623/working/building/REAL300000042075 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/82
`/scratch/stefan/7769623/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=C1)

`REAL300000042075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042075 none O=C([O-])C1=CC=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 11, 38, 38, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 11, 38, 47, 47, 47, 47, 47, 47, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
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: REAL300000042075 none O=C([O-])C1=CC=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 31, 12, 12, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 47, 47, 47, 47, 30, 12, 3, 1, 1, 1, 1, 1, 47] 47
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 99
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042075 none O=C([O-])C1=CC=CC(NN=CC2=COC(C3=CC=CC=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 24, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 47, 47, 47, 47, 24, 5, 1, 3, 3, 2, 3, 3, 47] 47
rigid atoms, others: [10, 11, 12, 13, 14, 15, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042075 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042075
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042075/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042075
Building REAL300000042076
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042076'
/scratch/stefan/7769623/working/building/REAL300000042076 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042076

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042076/0 /scratch/stefan/7769623/working/building/REAL300000042076 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/83
`/scratch/stefan/7769623/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042076 none CC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 52, 52, 151, 174, 174, 174, 174, 174, 174, 174, 174, 1, 2, 2, 2, 1, 1, 1, 11, 11, 52, 151, 174, 174, 174, 174, 1] 174
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 430
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: REAL300000042076 none CC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 174, 174, 174, 174, 89, 89, 89, 89, 89, 37, 37, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 174, 174, 174, 174, 174, 174, 174, 89, 89, 37, 7, 1, 1, 1, 1, 174] 174
rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 277
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042076 none CC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 12, 49, 89, 89, 89, 89, 89, 89, 89, 89, 11, 11, 11, 11, 11, 11, 11, 1, 1, 12, 49, 89, 89, 89, 89, 11] 174
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 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])
total number of confs: 193
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042076 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042076
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042076/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042076
Building REAL300000042077
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042077'
/scratch/stefan/7769623/working/building/REAL300000042077 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042077

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042077/0 /scratch/stefan/7769623/working/building/REAL300000042077 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/84
`/scratch/stefan/7769623/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-])

`REAL300000042077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042077 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 7, 7, 26, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 2, 2, 1, 1, 1, 7, 15, 23, 23, 3, 3, 3, 1, 7, 26, 71, 71, 71, 71, 1, 15, 15] 192
rigid atoms, others: [1, 2, 3, 4, 5, 38, 17, 18, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 212
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042077 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 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: [118, 71, 71, 71, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 71, 71, 71, 71, 71, 166, 192, 192, 192, 118, 118, 118, 71, 35, 8, 1, 1, 1, 1, 71, 192, 192] 192
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 486
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042077 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042077
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042077/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042077
Building REAL300000042078
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042078'
/scratch/stefan/7769623/working/building/REAL300000042078 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042078

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042078/0 /scratch/stefan/7769623/working/building/REAL300000042078 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/85
`/scratch/stefan/7769623/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1)

`REAL300000042078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042078 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 46, 46, 61, 61, 61, 114, 114, 97, 114, 114, 114, 114, 61, 61, 1, 1, 1, 1, 11, 46, 61, 114, 114, 114, 1] 114
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 272
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042078 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 114, 114, 114, 114, 86, 27, 27, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 114, 114, 114, 114, 86, 27, 11, 1, 1, 1, 114] 114
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 248
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042078 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [61, 61, 61, 61, 61, 61, 61, 28, 7, 7, 1, 1, 1, 1, 1, 11, 11, 2, 7, 11, 11, 11, 1, 1, 61, 61, 61, 61, 28, 7, 1, 11, 11, 11, 61] 114
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042078 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042078/1 /scratch/stefan/7769623/working/building/REAL300000042078 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/86
`/scratch/stefan/7769623/working/3D/86' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1)

`REAL300000042078.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042078/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042078 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 104, 104, 104, 201, 201, 104, 201, 201, 201, 201, 104, 104, 1, 1, 1, 1, 38, 39, 104, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 716
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042078 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 155, 155, 41, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 201, 201, 201, 201, 41, 41, 8, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 367
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042078 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(Cl)C=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 16, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 55, 55, 9, 1, 1, 1, 1, 1, 8, 8, 1, 3, 8, 8, 8, 1, 1, 104, 104, 104, 104, 9, 9, 1, 8, 8, 8, 104] 201
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 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
/scratch/stefan/7769623/working/building/REAL300000042078 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042078
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042078/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042078/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042078
Building REAL300000042079
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042079'
/scratch/stefan/7769623/working/building/REAL300000042079 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042079

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042079/0 /scratch/stefan/7769623/working/building/REAL300000042079 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/87
`/scratch/stefan/7769623/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3CCCO3)S2)=C1)

`REAL300000042079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042079 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3CCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 62, 111, 111, 111, 111, 201, 201, 201, 201, 111, 1, 1, 1, 1, 13, 62, 111, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 444
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042079 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3CCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 165, 52, 52, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 165, 52, 12, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 35])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042079 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3CCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 43, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 111, 111, 111, 111, 43, 8, 1, 12, 12, 12, 12, 12, 12, 12, 111] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042079 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042079
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042079/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042079
Building REAL300000042080
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042080'
/scratch/stefan/7769623/working/building/REAL300000042080 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042080

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042080/0 /scratch/stefan/7769623/working/building/REAL300000042080 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/88
`/scratch/stefan/7769623/working/3D/88' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CC3CCCC4=CC=CC2=C43)=C1)

`REAL300000042080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042080 none O=C([O-])C1=CC=CC(NN=C2CC3CCCC4=CC=CC2=C43)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 33
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042080 none O=C([O-])C1=CC=CC(NN=C2CC3CCCC4=CC=CC2=C43)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 19
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24, 25, 26])
total number of confs: 33
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042080 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042080
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042080/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042080
Building REAL300000042081
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042081'
/scratch/stefan/7769623/working/building/REAL300000042081 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042081

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042081/0 /scratch/stefan/7769623/working/building/REAL300000042081 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/89
`/scratch/stefan/7769623/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042081 none CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [2, 1, 2, 2, 1, 1, 1, 1, 10, 10, 1, 10, 10, 11, 1, 1, 1, 8, 8, 29, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 1, 10, 1, 8, 29, 42, 42, 42, 42] 85
rigid atoms, others: [1, 4, 5, 6, 7, 41, 14, 15, 16] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47])
total number of confs: 118
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: REAL300000042081 none CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [42, 42, 42, 42, 42, 42, 42, 42, 85, 85, 42, 85, 85, 85, 42, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 85, 85, 85, 85, 42, 28, 8, 1, 1, 1, 1] 85
rigid atoms, others: [44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 287
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042081 none CC(C)(C)C1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [11, 10, 11, 11, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 38, 38, 78, 85, 85, 85, 85, 85, 85, 85, 85, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 10, 38, 78, 85, 85, 85, 85] 85
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 205
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042081 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042081
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042081/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042081
Building REAL300000042082
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042082'
/scratch/stefan/7769623/working/building/REAL300000042082 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042082

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042082/0 /scratch/stefan/7769623/working/building/REAL300000042082 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/90
`/scratch/stefan/7769623/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(Br)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042082 none CC1=NN(C2=CC=C(Br)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 1, 3, 3, 3, 1, 1, 1, 6, 6, 55, 102, 102, 102, 102, 102, 103, 103, 102, 2, 2, 2, 3, 3, 3, 3, 1, 6, 55, 102, 102, 102, 102] 103
rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042082 none CC1=NN(C2=CC=C(Br)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [102, 102, 102, 102, 102, 102, 102, 100, 102, 102, 102, 102, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 103, 103, 103, 102, 102, 103, 103, 102, 54, 12, 1, 1, 1, 1] 103
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 171
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042082 none CC1=NN(C2=CC=C(Br)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 16, 75, 102, 102, 102, 102, 103, 103, 103, 102, 4, 4, 4, 1, 1, 1, 1, 3, 16, 76, 102, 102, 102, 103] 103
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042082 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042082
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042082/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042082
Building REAL300000042083
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042083'
/scratch/stefan/7769623/working/building/REAL300000042083 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042083

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042083/0 /scratch/stefan/7769623/working/building/REAL300000042083 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/91
`/scratch/stefan/7769623/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042083 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 9, 19, 19, 13, 19, 19, 1, 1, 1, 8, 8, 38, 77, 77, 77, 77, 77, 77, 77, 77, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 19, 19, 19, 19, 19, 1, 8, 38, 77, 77, 77, 77] 201
rigid atoms, others: [1, 4, 5, 6, 7, 44, 14, 15, 16] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50])
total number of confs: 232
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: REAL300000042083 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 77, 191, 201, 201, 201, 201, 201, 77, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 191, 191, 201, 201, 201, 201, 201, 77, 33, 8, 1, 1, 1, 1] 201
rigid atoms, others: [50, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 607
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042083 none CC(C)(C)C1=NN(CC2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 19, 20, 20, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 75, 75, 174, 201, 201, 201, 201, 201, 201, 201, 201, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 19, 75, 174, 201, 201, 201, 201] 201
rigid atoms, others: [11, 39, 8, 9, 10, 7, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 490
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042083 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042083
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042083/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042083
Building REAL300000042084
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042084'
/scratch/stefan/7769623/working/building/REAL300000042084 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042084

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042084/0 /scratch/stefan/7769623/working/building/REAL300000042084 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/92
`/scratch/stefan/7769623/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1)

`REAL300000042084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042084 none CSC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 9, 9, 9, 48, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 1, 11, 11, 11, 1, 1, 9, 9, 9, 48, 159, 159, 159, 159, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 272
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042084 none CSC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 99, 80, 159, 159, 54, 54, 54, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 159, 159, 159, 201, 201, 201, 159, 159, 55, 55, 55, 11, 1, 1, 1, 1, 159] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 595
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042084 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042084
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042084/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042084
Building REAL300000042085
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042085'
/scratch/stefan/7769623/working/building/REAL300000042085 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042085

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042085/0 /scratch/stefan/7769623/working/building/REAL300000042085 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/93
`/scratch/stefan/7769623/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl)

`REAL300000042085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042085 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 59, 59, 35, 59, 59, 59, 59, 36, 36, 36, 10, 1, 1, 1, 1, 59, 59, 59] 59
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 222
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042085 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 37, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 59, 59, 59, 59, 1, 1, 1] 59
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 123
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042085 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042085
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042085/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042085
Building REAL300000042086
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042086'
/scratch/stefan/7769623/working/building/REAL300000042086 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042086

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042086/0 /scratch/stefan/7769623/working/building/REAL300000042086 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/94
`/scratch/stefan/7769623/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC=CC=C2C(F)(F)F)=C1)

`REAL300000042086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042086 none O=C([O-])C1=CC=CC(NN=CC2=NC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 13, 46, 46, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 13, 46, 62, 62, 62, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 100
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042086 none O=C([O-])C1=CC=CC(NN=CC2=NC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 62, 62, 62, 62, 34, 5, 1, 1, 1, 62] 62
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042086 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042086
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042086/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042086
Building REAL300000042087
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042087'
/scratch/stefan/7769623/working/building/REAL300000042087 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042087

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042087/0 /scratch/stefan/7769623/working/building/REAL300000042087 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/95
`/scratch/stefan/7769623/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(S1)SCC(=O)N2)

`REAL300000042087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042087 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(S1)SCC(=O)N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 14, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 65, 65, 65, 65, 65, 65, 65, 65, 65, 45, 45, 45, 10, 1, 1, 1, 1, 65, 65, 65, 65] 65
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 111
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042087 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(S1)SCC(=O)N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 14, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [12, 1, 12, 12, 41, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 41, 65, 65, 65, 65, 1, 1, 1, 1] 65
rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 134
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042087 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042087
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042087/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042087
Building REAL300000042088
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042088'
/scratch/stefan/7769623/working/building/REAL300000042088 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042088

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042088/0 /scratch/stefan/7769623/working/building/REAL300000042088 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/96
`/scratch/stefan/7769623/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(F)=C1)

`REAL300000042088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042088 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 98, 98, 98, 98, 98, 98, 98, 52, 52, 52, 10, 1, 1, 1, 1, 98, 98, 98] 98
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 159
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042088 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 1, 10, 10, 52, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 98, 98, 98, 98, 1, 1, 1] 98
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 201
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042088 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042088
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042088/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042088
Building REAL300000042089
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042089'
/scratch/stefan/7769623/working/building/REAL300000042089 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042089

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042089/0 /scratch/stefan/7769623/working/building/REAL300000042089 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/97
`/scratch/stefan/7769623/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042089 none CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 7, 7, 41, 83, 83, 83, 83, 83, 83, 83, 83, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 1, 5, 5, 7, 40, 83, 83, 83, 82] 99
rigid atoms, others: [1, 4, 5, 6, 7, 13, 14, 15, 16] set([0, 2, 3, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 179
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: REAL300000042089 none CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [91, 83, 91, 91, 82, 82, 82, 82, 99, 99, 83, 99, 99, 82, 83, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 91, 91, 91, 91, 91, 91, 91, 91, 91, 99, 99, 84, 99, 99, 36, 8, 1, 1, 1, 1] 99
rigid atoms, others: [44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 260
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042089 none CC(C)(C)C1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 27, 27, 68, 99, 99, 99, 99, 99, 99, 99, 99, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 27, 68, 99, 99, 99, 99] 99
rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 40, 41, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47])
total number of confs: 262
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042089 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042089
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042089/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042089
Building REAL300000042090
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042090'
/scratch/stefan/7769623/working/building/REAL300000042090 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042090

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042090/0 /scratch/stefan/7769623/working/building/REAL300000042090 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/98
`/scratch/stefan/7769623/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(N)C(Cl)=C1)

`REAL300000042090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042090 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(N)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 56, 56, 56, 56, 56, 56, 56, 56, 38, 38, 38, 10, 1, 1, 1, 1, 56, 56, 56, 56] 56
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 101
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042090 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(N)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 27, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 56, 56, 56, 56, 1, 2, 2, 1] 56
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 118
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042090 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042090
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042090/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042090
Building REAL300000042091
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042091'
/scratch/stefan/7769623/working/building/REAL300000042091 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042091

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042091/0 /scratch/stefan/7769623/working/building/REAL300000042091 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/99
`/scratch/stefan/7769623/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CO2)C=C1)

`REAL300000042091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042091 none CC1=CC=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 17, 39, 51, 51, 52, 52, 52, 52, 52, 52, 4, 4, 1, 1, 2, 2, 2, 1, 1, 17, 39, 51, 51, 52, 52, 4, 1, 1] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 36, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042091 none CC1=CC=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 51, 51, 51, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 51, 51, 52, 52, 52, 52, 52, 51, 36, 10, 1, 1, 1, 1, 52, 51, 52] 52
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37])
total number of confs: 96
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042091 none CC1=CC=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CO2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [2, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 31, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 3, 3, 4, 4, 4, 3, 3, 6, 30, 52, 52, 52, 51, 1, 3, 3] 52
rigid atoms, others: [35, 4, 5, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 122
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042091 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042091
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042091/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042091
Building REAL300000042092
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042092'
/scratch/stefan/7769623/working/building/REAL300000042092 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042092

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042092/0 /scratch/stefan/7769623/working/building/REAL300000042092 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/100
`/scratch/stefan/7769623/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Cl)=CC(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042092 none CC1=CC(Cl)=CC(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 2, 2, 2, 7, 23, 43, 43, 43, 43] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042092 none CC1=CC(Cl)=CC(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 32, 32, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 43, 43, 43, 43, 43, 32, 12, 1, 1, 1, 1] 43
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042092 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042092
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042092/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042092
Building REAL300000042093
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042093'
/scratch/stefan/7769623/working/building/REAL300000042093 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042093

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042093/0 /scratch/stefan/7769623/working/building/REAL300000042093 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/101
`/scratch/stefan/7769623/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C1=CC=CC=C1)

`REAL300000042093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042093 none CC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 71, 154, 154, 154, 154, 154, 154, 154, 153, 1, 1, 4, 4, 2, 4, 4, 2, 2, 2, 1, 12, 70, 154, 154, 154, 153, 4, 4, 3, 4, 4] 154
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042093 none CC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 27, 27, 101, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 27, 101, 154, 154, 154, 154, 1, 1, 1, 1, 1] 154
rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 331
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042093 none CC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 153, 153, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 153, 154, 154, 154, 154, 154, 154, 154, 154, 154, 153, 63, 12, 1, 1, 1, 1, 154, 154, 154, 154, 154] 154
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042093 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042093
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042093/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042093
Building REAL300000042094
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042094'
/scratch/stefan/7769623/working/building/REAL300000042094 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042094

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042094/0 /scratch/stefan/7769623/working/building/REAL300000042094 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/102
`/scratch/stefan/7769623/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1N=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1C)

`REAL300000042094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042094 none CCCN1N=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 56, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 10, 10, 10, 9, 9, 5, 5, 2, 2, 2, 11, 56, 107, 107, 107, 107, 2, 2, 2] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042094 none CCCN1N=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 107, 107, 107, 107, 107, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 107, 107, 201, 201, 201, 201, 201, 199, 199, 107, 107, 107, 34, 8, 1, 1, 1, 1, 107, 107, 107] 201
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 626
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042094 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042094
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042094/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042094
Building REAL300000042095
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042095'
/scratch/stefan/7769623/working/building/REAL300000042095 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042095

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042095/0 /scratch/stefan/7769623/working/building/REAL300000042095 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/103
`/scratch/stefan/7769623/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042095 none CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 1, 1, 3, 3, 1, 1, 1, 6, 6, 57, 102, 102, 102, 102, 102, 103, 103, 102, 2, 2, 2, 3, 3, 3, 3, 1, 6, 57, 102, 102, 102, 102] 103
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 32] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042095 none CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [102, 102, 102, 102, 102, 102, 102, 100, 102, 102, 102, 102, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 103, 103, 103, 102, 102, 102, 102, 102, 53, 12, 1, 1, 1, 1] 103
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 172
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042095 none CC1=NN(C2=CC=C(Cl)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 16, 74, 102, 102, 102, 103, 103, 103, 103, 103, 4, 4, 4, 1, 1, 1, 1, 3, 16, 75, 102, 102, 102, 103] 103
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042095 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042095
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042095/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042095
Building REAL300000042096
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042096'
/scratch/stefan/7769623/working/building/REAL300000042096 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042096

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042096/0 /scratch/stefan/7769623/working/building/REAL300000042096 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/104
`/scratch/stefan/7769623/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=C1)

`REAL300000042096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042096 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 101, 101, 101, 101, 101, 194, 194, 194, 194, 194, 194, 1, 1, 1, 1, 7, 37, 101, 101, 194, 194, 194, 194, 1] 194
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 293
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: REAL300000042096 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 194, 194, 194, 194, 194, 173, 64, 64, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 173, 64, 11, 11, 1, 1, 1, 1, 194] 194
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 466
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042096 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 101, 101, 101, 57, 13, 13, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 101, 101, 101, 101, 57, 13, 1, 1, 11, 11, 11, 11, 101] 194
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 216
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042096 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042096
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042096/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042096
Building REAL300000042097
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042097'
/scratch/stefan/7769623/working/building/REAL300000042097 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042097

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042097/0 /scratch/stefan/7769623/working/building/REAL300000042097 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/105
`/scratch/stefan/7769623/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1)

`REAL300000042097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042097 none O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 97, 97, 1, 1, 1, 1, 23, 24, 201, 201, 201, 97, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042097 none O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 161, 161, 44, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 44, 44, 1, 1, 1, 7, 201] 201
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 376
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042097 none O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 97, 96, 97, 97, 54, 54, 8, 1, 1, 1, 1, 1, 7, 7, 7, 2, 7, 7, 7, 1, 1, 97, 96, 97, 97, 8, 8, 7, 2, 7, 1, 97] 201
rigid atoms, others: [33, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042097 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042097/1 /scratch/stefan/7769623/working/building/REAL300000042097 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/106
`/scratch/stefan/7769623/working/3D/106' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1)

`REAL300000042097.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042097/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042097 none O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 60, 60, 113, 113, 112, 201, 201, 201, 201, 201, 201, 201, 113, 113, 1, 1, 1, 1, 11, 60, 201, 201, 201, 113, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 311
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042097 none O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 160, 42, 42, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 201, 201, 201, 201, 160, 42, 1, 1, 1, 10, 201] 201
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042097 none O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC(Cl)=CC=C3Cl)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 113, 113, 113, 49, 9, 9, 1, 1, 1, 1, 1, 10, 10, 10, 2, 10, 10, 10, 1, 1, 113, 113, 113, 113, 49, 9, 10, 2, 10, 1, 113] 201
rigid atoms, others: [33, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34])
total number of confs: 227
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042097 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042097
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042097/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042097/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042097
Building REAL300000042098
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042098'
/scratch/stefan/7769623/working/building/REAL300000042098 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042098

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042098/0 /scratch/stefan/7769623/working/building/REAL300000042098 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/107
`/scratch/stefan/7769623/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042098 none CN1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 76, 76, 76, 76, 76, 77, 77, 76, 2, 2, 2, 1, 1, 1, 8, 8, 76, 76, 76, 76] 77
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042098 none CN1C2=CC=C(Cl)C=C2N=C1CN=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 77, 77, 76, 76, 76, 39, 39, 1, 1, 1, 1] 77
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042098 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042098/1 /scratch/stefan/7769623/working/building/REAL300000042098 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/108
`/scratch/stefan/7769623/working/3D/108' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC2=CC(Cl)=CC=C21)

`REAL300000042098.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042098/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042098 none CN1C(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC2=CC(Cl)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 40, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 40, 56, 56, 56, 56, 1, 1, 1] 56
rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042098 none CN1C(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC2=CC(Cl)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 38, 12, 1, 1, 1, 1, 56, 56, 56] 56
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042098 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042098
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042098/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042098/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042098
Building REAL300000042099
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042099'
/scratch/stefan/7769623/working/building/REAL300000042099 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042099

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042099/0 /scratch/stefan/7769623/working/building/REAL300000042099 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/109
`/scratch/stefan/7769623/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=C1)

`REAL300000042099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042099 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 79, 79, 79, 79, 79, 135, 135, 135, 135, 135, 135, 1, 1, 1, 1, 7, 33, 79, 79, 135, 135, 135, 135, 1] 135
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042099 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 135, 135, 135, 135, 117, 37, 37, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 117, 37, 11, 11, 1, 1, 1, 1, 135] 135
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 327
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042099 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=CC=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 79, 79, 79, 79, 45, 9, 1, 1, 11, 11, 11, 11, 79] 135
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042099 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042099
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042099/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042099
Building REAL300000042100
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042100'
/scratch/stefan/7769623/working/building/REAL300000042100 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042100

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042100/0 /scratch/stefan/7769623/working/building/REAL300000042100 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/110
`/scratch/stefan/7769623/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=C1)

`REAL300000042100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042100 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 74, 74, 178, 178, 178, 178, 178, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 13, 74, 178, 178, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 291
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042100 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 81, 29, 29, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 81, 29, 8, 8, 1, 1, 1, 96] 96
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 227
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042100 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2C2=C(F)C=CC=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [178, 178, 178, 178, 178, 178, 178, 74, 13, 13, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 178, 178, 178, 178, 74, 13, 1, 1, 6, 6, 6, 178] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 327
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042100 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042100
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042100/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042100
Building REAL300000042101
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042101'
/scratch/stefan/7769623/working/building/REAL300000042101 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042101

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042101/0 /scratch/stefan/7769623/working/building/REAL300000042101 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/111
`/scratch/stefan/7769623/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042101 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 10, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 9, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 10, 10, 1, 1, 1, 4, 9, 24, 24, 24, 24] 30
rigid atoms, others: [1, 34, 35, 33, 6, 7, 8, 9, 10, 14, 15, 16] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41])
total number of confs: 98
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042101 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [29, 24, 29, 30, 30, 30, 24, 24, 18, 24, 24, 24, 24, 24, 24, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 30, 30, 24, 24, 24, 18, 7, 1, 1, 1, 1] 30
rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 99
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042101 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042101
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042101/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042101
Building REAL300000042102
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042102'
/scratch/stefan/7769623/working/building/REAL300000042102 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042102

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042102/0 /scratch/stefan/7769623/working/building/REAL300000042102 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/112
`/scratch/stefan/7769623/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1)

`REAL300000042102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042102 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 52, 52, 66, 66, 66, 116, 116, 116, 116, 116, 116, 116, 66, 66, 1, 1, 1, 1, 11, 52, 65, 116, 116, 116, 1] 116
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042102 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 116, 116, 116, 116, 116, 116, 83, 24, 24, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 116, 116, 116, 116, 83, 24, 10, 1, 1, 1, 116] 116
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 251
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042102 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 66, 66, 66, 66, 66, 66, 25, 7, 7, 1, 1, 1, 1, 1, 10, 10, 3, 10, 10, 10, 10, 1, 1, 66, 66, 66, 66, 25, 7, 1, 10, 10, 9, 66] 116
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042102 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042102/1 /scratch/stefan/7769623/working/building/REAL300000042102 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/113
`/scratch/stefan/7769623/working/3D/113' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1)

`REAL300000042102.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042102/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042102 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 45, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 1, 1, 1, 1, 44, 45, 119, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 380
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042102 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 152, 152, 36, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 36, 36, 7, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 357
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042102 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC(Cl)=C3Cl)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 16, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 119, 119, 119, 119, 52, 52, 9, 1, 1, 1, 1, 1, 7, 7, 5, 7, 7, 7, 7, 1, 1, 119, 119, 119, 119, 9, 9, 1, 7, 7, 7, 119] 201
rigid atoms, others: [10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042102 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042102
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042102/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042102/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042102
Building REAL300000042103
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042103'
/scratch/stefan/7769623/working/building/REAL300000042103 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042103

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042103/0 /scratch/stefan/7769623/working/building/REAL300000042103 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/114
`/scratch/stefan/7769623/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=C1)

`REAL300000042103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042103 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 54, 54, 89, 89, 123, 123, 89, 89, 89, 89, 89, 66, 1, 1, 1, 1, 11, 54, 123, 123, 123, 123, 123, 89, 89, 1] 123
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042103 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 123, 123, 123, 123, 91, 30, 30, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 123, 123, 123, 123, 91, 30, 1, 1, 1, 1, 1, 8, 8, 123] 123
rigid atoms, others: [32, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 279
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042103 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N=C3SC=CN23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 14, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [89, 89, 89, 89, 89, 89, 89, 42, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 42, 8, 8, 8, 8, 8, 8, 1, 1, 89] 123
rigid atoms, others: [33, 34, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042103 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042103
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042103/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042103
Building REAL300000042104
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042104'
/scratch/stefan/7769623/working/building/REAL300000042104 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042104

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042104/0 /scratch/stefan/7769623/working/building/REAL300000042104 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/115
`/scratch/stefan/7769623/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=C1)

`REAL300000042104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042104 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 48, 48, 114, 114, 114, 114, 114, 114, 48, 1, 1, 1, 1, 48, 48, 48, 48, 114, 114, 114, 114, 48, 48, 1] 114
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 197
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: REAL300000042104 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 114, 114, 114, 114, 75, 75, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 114, 114, 114, 114, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 114] 114
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 172
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042104 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 13, 13, 1, 1, 1, 1, 1, 13, 13, 5, 13, 13, 13, 1, 48, 48, 48, 48, 1, 1, 1, 1, 13, 13, 12, 13, 1, 1, 48] 114
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 32, 35])
total number of confs: 104
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042104 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042104
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042104/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042104
Building REAL300000042105
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042105'
/scratch/stefan/7769623/working/building/REAL300000042105 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042105

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042105/0 /scratch/stefan/7769623/working/building/REAL300000042105 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/116
`/scratch/stefan/7769623/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1)

`REAL300000042105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042105 none O=C([O-])C1=CC=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 67, 106, 187, 201, 201, 191, 201, 201, 18, 29, 29, 25, 29, 29, 29, 1, 1, 1, 1, 4, 67, 67, 187, 187, 201, 201, 201, 201, 201, 29, 29, 29, 29, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 795
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042105 none O=C([O-])C1=CC=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 12, 4, 4, 1, 4, 25, 48, 105, 155, 155, 118, 155, 155, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 12, 25, 25, 105, 105, 155, 155, 155, 155, 155, 1, 1, 1, 1, 29] 201
rigid atoms, others: [41, 10, 43, 44, 20, 21, 22, 23, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 659
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042105 none O=C([O-])C1=CC=CC(NN=C(COCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 187, 116, 116, 51, 13, 3, 1, 1, 1, 1, 1, 1, 1, 116, 155, 155, 145, 155, 155, 155, 201, 201, 201, 201, 187, 51, 51, 3, 3, 1, 1, 1, 1, 1, 155, 155, 155, 155, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042105 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042105
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042105/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042105
Building REAL300000042106
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042106'
/scratch/stefan/7769623/working/building/REAL300000042106 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042106

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042106/0 /scratch/stefan/7769623/working/building/REAL300000042106 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/117
`/scratch/stefan/7769623/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NN(C)C(CC)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042106 none CCC1=NN(C)C(CC)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 13, 13, 60, 92, 92, 92, 92, 92, 92, 92, 92, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 3, 3, 3, 13, 60, 92, 92, 92, 92] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042106 none CCC1=NN(C)C(CC)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 92, 92, 92, 92, 92, 92, 152, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 124, 124, 124, 124, 124, 92, 92, 92, 152, 152, 152, 152, 152, 26, 8, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 685
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042106 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042106
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042106/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042106
Building REAL300000042107
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042107'
/scratch/stefan/7769623/working/building/REAL300000042107 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042107

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042107/0 /scratch/stefan/7769623/working/building/REAL300000042107 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/118
`/scratch/stefan/7769623/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=C1)

`REAL300000042107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042107 none O=C([O-])C1=CC=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 34, 34, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 11, 34, 41, 41, 41, 41, 41, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042107 none O=C([O-])C1=CC=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 25, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 41, 41, 25, 7, 1, 1, 1, 1, 1, 3, 3, 41] 41
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 83
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042107 none O=C([O-])C1=CC=CC(NN=CC2=NN(C3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 40, 41, 41, 23, 4, 4, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 41, 40, 41, 41, 23, 4, 3, 3, 1, 3, 3, 1, 1, 41] 41
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042107 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042107
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042107/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042107
Building REAL300000042108
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042108'
/scratch/stefan/7769623/working/building/REAL300000042108 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042108

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042108/0 /scratch/stefan/7769623/working/building/REAL300000042108 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/119
`/scratch/stefan/7769623/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042108 none CCC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 59, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 71, 59, 28, 28, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 545
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042108 none CCC(CSC1=CC=CC=C1[N+](=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 8, 40, 77, 158, 201, 201, 180, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 49, 40, 77, 77, 201, 201, 180, 201, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 656
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042108 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042108
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042108/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042108
Building REAL300000042109
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042109'
/scratch/stefan/7769623/working/building/REAL300000042109 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042109

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042109/0 /scratch/stefan/7769623/working/building/REAL300000042109 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/120
`/scratch/stefan/7769623/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN2C(=NC(C(C)C)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042109 none CC1=NN2C(=NC(C(C)C)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 72, 118, 118, 118, 118, 118, 118, 118, 118, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 12, 72, 118, 118, 118, 118] 118
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 23] set([8, 9, 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, 38, 39])
total number of confs: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042109 none CC1=NN2C(=NC(C(C)C)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 8, 1, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 47, 13, 1, 1, 1, 1] 118
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042109 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042109
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042109/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042109
Building REAL300000042110
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042110'
/scratch/stefan/7769623/working/building/REAL300000042110 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042110

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042110/0 /scratch/stefan/7769623/working/building/REAL300000042110 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/121
`/scratch/stefan/7769623/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)NCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1)

`REAL300000042110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042110 none CS(=O)(=O)NCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 201, 83, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 36, 36, 18, 36, 36, 201, 201, 201, 173, 83, 83, 4, 1, 1, 1, 1, 36, 36, 18, 36, 36] 201
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 785
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042110 none CS(=O)(=O)NCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 88, 139, 139, 25, 4, 1, 4, 4, 15, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 139, 139, 139, 88, 25, 25, 15, 36, 36, 36, 36, 1, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 6, 39, 18, 19, 20, 21, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 569
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042110 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042110
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042110/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042110
Building REAL300000042111
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042111'
/scratch/stefan/7769623/working/building/REAL300000042111 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042111

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042111/0 /scratch/stefan/7769623/working/building/REAL300000042111 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/122
`/scratch/stefan/7769623/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC2=C(CCCC2)S1)

`REAL300000042111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042111 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC2=C(CCCC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 124, 124, 124, 124, 124, 124, 124, 124, 43, 43, 43, 43, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 124, 124] 124
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 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: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042111 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC2=C(CCCC2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 89, 89, 124, 124, 124, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1] 124
rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 195
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042111 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042111
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042111/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042111
Building REAL300000042112
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042112'
/scratch/stefan/7769623/working/building/REAL300000042112 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042112

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042112/0 /scratch/stefan/7769623/working/building/REAL300000042112 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/123
`/scratch/stefan/7769623/working/3D/123' -> `0.mol2'
Preparing input files

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

`REAL300000042112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042112 none CC(CC1=CC=CC=C1[N+](=O)[O-])C(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 36, 36, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 36, 36, 36, 36, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 399
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042112 none CC(CC1=CC=CC=C1[N+](=O)[O-])C(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 58, 143, 184, 201, 201, 201, 201, 201, 201, 201, 201, 8, 58, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 150, 150, 150, 150, 184, 184, 201, 201, 201, 201, 58, 58, 58, 58, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 866
number of broken/clashed sets: 94
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042112 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042112
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042112/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042112
Building REAL300000042113
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042113'
/scratch/stefan/7769623/working/building/REAL300000042113 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042113

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042113/0 /scratch/stefan/7769623/working/building/REAL300000042113 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/124
`/scratch/stefan/7769623/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Br)

`REAL300000042113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042113 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 9, 9, 50, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 2, 2, 2, 1, 1, 9, 50, 67, 67, 67, 67, 1] 67
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042113 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [66, 66, 67, 67, 39, 39, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 67, 67, 67, 67, 67, 67, 39, 12, 1, 1, 1, 1, 67] 67
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 126
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042113 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042113
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042113/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042113
Building REAL300000042114
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042114'
/scratch/stefan/7769623/working/building/REAL300000042114 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042114

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042114/0 /scratch/stefan/7769623/working/building/REAL300000042114 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/125
`/scratch/stefan/7769623/working/3D/125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCOC3=CC(Br)=CC=C32)=C1)

`REAL300000042114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042114 none O=C([O-])C1=CC=CC(NN=C2CCOC3=CC(Br)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 37
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042114 none O=C([O-])C1=CC=CC(NN=C2CCOC3=CC(Br)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 33])
total number of confs: 35
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042114 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042114
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042114/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042114
Building REAL300000042115
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042115'
/scratch/stefan/7769623/working/building/REAL300000042115 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042115

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042115/0 /scratch/stefan/7769623/working/building/REAL300000042115 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/126
`/scratch/stefan/7769623/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1[N+](=O)[O-])

`REAL300000042115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042115 none CCOC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 1, 2, 2, 19, 19, 19, 19, 19, 1, 1, 13, 13, 13, 67, 134, 134, 134, 134, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 20, 21, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 316
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042115 none CCOC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 180, 64, 35, 134, 134, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 134, 134, 134, 134, 134, 201, 201, 201, 201, 201, 134, 134, 32, 32, 32, 8, 1, 1, 1, 1, 134] 201
rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 676
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042115 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042115
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042115/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042115
Building REAL300000042116
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042116'
/scratch/stefan/7769623/working/building/REAL300000042116 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042116

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042116/0 /scratch/stefan/7769623/working/building/REAL300000042116 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/127
`/scratch/stefan/7769623/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2Br)=C1)

`REAL300000042116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042116 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 33, 33, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 11, 33, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042116 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 34, 10, 1, 1, 1, 45] 45
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042116 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042116
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042116/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042116
Building REAL300000042117
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042117'
/scratch/stefan/7769623/working/building/REAL300000042117 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042117

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042117/0 /scratch/stefan/7769623/working/building/REAL300000042117 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/128
`/scratch/stefan/7769623/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C(Br)C=C(Cl)C=C23)=C1)

`REAL300000042117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042117 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(Br)C=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 31
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042117 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(Br)C=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 17, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 17] 17
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 29
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042117 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042117
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042117/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042117
Building REAL300000042118
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042118'
/scratch/stefan/7769623/working/building/REAL300000042118 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042118

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042118/0 /scratch/stefan/7769623/working/building/REAL300000042118 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/129
`/scratch/stefan/7769623/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C(Cl)C=C(Br)C=C23)=C1)

`REAL300000042118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042118 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(Cl)C=C(Br)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 27
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042118 none O=C([O-])C1=CC=CC(NN=C2CCC3=C(Cl)C=C(Br)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 16, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 27
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042118 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042118
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042118/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042118
Building REAL300000042119
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042119'
/scratch/stefan/7769623/working/building/REAL300000042119 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042119

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042119/0 /scratch/stefan/7769623/working/building/REAL300000042119 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/130
`/scratch/stefan/7769623/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1[O-])

`REAL300000042119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042119 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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: [21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 6, 1, 1, 1, 1, 25, 25, 25] 25
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 46
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042119 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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: [5, 1, 5, 5, 17, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 17, 25, 25, 25, 25, 1, 1, 1] 25
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 57
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042119 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042119
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042119/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042119
Building REAL300000042120
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042120'
/scratch/stefan/7769623/working/building/REAL300000042120 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042120

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042120/0 /scratch/stefan/7769623/working/building/REAL300000042120 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/131
`/scratch/stefan/7769623/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C(C)(C)C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042120 none CC1=NN(C(C)(C)C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 10, 51, 77, 77, 77, 77, 77, 77, 77, 76, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 51, 77, 77, 77, 76] 77
rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 187
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042120 none CC1=NN(C(C)(C)C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 76, 76, 76, 76, 77, 77, 77, 76, 77, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 38, 10, 1, 1, 1, 1] 77
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 134
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042120 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042120
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042120/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042120
Building REAL300000042121
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042121'
/scratch/stefan/7769623/working/building/REAL300000042121 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042121

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042121/0 /scratch/stefan/7769623/working/building/REAL300000042121 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/132
`/scratch/stefan/7769623/working/3D/132' -> `0.mol2'
Preparing input files

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

`REAL300000042121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042121 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 45, 45, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 13, 45, 77, 77, 77, 1] 77
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042121 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 77, 77, 77, 76, 77, 77, 52, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 77, 76, 77, 77, 52, 10, 1, 1, 1, 77] 77
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042121 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042121
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042121/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042121
Building REAL300000042122
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042122'
/scratch/stefan/7769623/working/building/REAL300000042122 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042122

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042122/0 /scratch/stefan/7769623/working/building/REAL300000042122 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/133
`/scratch/stefan/7769623/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCCC1C1CCCC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042122 none CC(C)(C)OC(=O)N1CCCC1C1CCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 15, 19, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 24, 24, 78, 78, 78, 78, 78, 78, 78, 78, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 78, 78, 78, 78] 145
rigid atoms, others: [43, 37, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 5] 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, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 152
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042122 none CC(C)(C)OC(=O)N1CCCC1C1CCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 145, 145, 126, 78, 126, 78, 78, 78, 78, 43, 43, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 145, 145, 145, 145, 145, 145, 145, 145, 145, 78, 78, 78, 78, 78, 78, 78, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1] 145
rigid atoms, others: [54, 55, 18, 19, 52, 21, 22, 23, 24, 20, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 423
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042122 none CC(C)(C)OC(=O)N1CCCC1C1CCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 25, 30, 30, 11, 4, 11, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 43, 43, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43] 145
rigid atoms, others: [48, 17, 47, 12, 11, 44, 13, 14, 45, 16, 49, 50, 51, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 52, 53, 54, 55])
total number of confs: 131
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042122 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042122
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042122/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042122
Building REAL300000042123
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042123'
/scratch/stefan/7769623/working/building/REAL300000042123 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042123

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042123/0 /scratch/stefan/7769623/working/building/REAL300000042123 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/134
`/scratch/stefan/7769623/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=C1)

`REAL300000042123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042123 none O=C([O-])C1=CC=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 44, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 68
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: REAL300000042123 none O=C([O-])C1=CC=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 19, 19, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 30, 30, 30, 30, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 30] 30
rigid atoms, others: [37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 44
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042123 none O=C([O-])C1=CC=CC(N=NC2CCCCC(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 30] 30
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 23, 24, 25, 26, 37, 38, 39, 40, 41, 44])
total number of confs: 46
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042123 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042123
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042123/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042123
Building REAL300000042124
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042124'
/scratch/stefan/7769623/working/building/REAL300000042124 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042124

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042124/0 /scratch/stefan/7769623/working/building/REAL300000042124 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/135
`/scratch/stefan/7769623/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(C(F)(F)F)=C2)=C1)

`REAL300000042124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042124 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 43, 43, 87, 87, 87, 77, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 13, 43, 87, 87, 87, 1] 87
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042124 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 86, 87, 87, 55, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 86, 87, 87, 55, 10, 1, 1, 1, 87] 87
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042124 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042124
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042124/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042124
Building REAL300000042125
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042125'
/scratch/stefan/7769623/working/building/REAL300000042125 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042125

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042125/0 /scratch/stefan/7769623/working/building/REAL300000042125 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/136
`/scratch/stefan/7769623/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042125 none CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 4, 2, 4, 4, 1, 1, 1, 6, 6, 55, 95, 96, 96, 95, 95, 96, 96, 95, 2, 2, 2, 4, 4, 2, 4, 4, 1, 6, 55, 95, 96, 96, 95] 96
rigid atoms, others: [0, 1, 2, 3, 4, 32, 10, 11, 12] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 209
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042125 none CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [95, 95, 95, 95, 95, 96, 96, 96, 96, 96, 95, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 96, 96, 96, 96, 96, 96, 96, 96, 95, 50, 12, 1, 1, 1, 1] 96
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 155
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042125 none CC1=NN(C2=CC=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 17, 71, 96, 96, 96, 96, 96, 96, 96, 96, 4, 4, 4, 1, 1, 1, 1, 1, 4, 17, 71, 96, 96, 96, 96] 96
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042125 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042125
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042125/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042125
Building REAL300000042126
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042126'
/scratch/stefan/7769623/working/building/REAL300000042126 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042126

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042126/0 /scratch/stefan/7769623/working/building/REAL300000042126 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/137
`/scratch/stefan/7769623/working/3D/137' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(OC)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042126 none COC1=CC=CC(OC)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 87, 167, 167, 167, 167, 167, 167, 167, 167, 3, 3, 3, 1, 1, 1, 3, 3, 3, 12, 87, 167, 167, 167, 167] 182
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10, 25, 26, 27] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 333
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042126 none COC1=CC=CC(OC)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [181, 155, 155, 155, 79, 155, 155, 155, 179, 56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 181, 181, 181, 155, 90, 155, 179, 179, 179, 56, 10, 1, 1, 1, 1] 182
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 501
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042126 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042126
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042126/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042126
Building REAL300000042127
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042127'
/scratch/stefan/7769623/working/building/REAL300000042127 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042127

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042127/0 /scratch/stefan/7769623/working/building/REAL300000042127 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/138
`/scratch/stefan/7769623/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042127 none CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 26, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 25, 36, 36, 36, 35] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13] set([7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 102
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: REAL300000042127 none CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 35, 35, 35, 35, 35, 36, 38, 38, 38, 38, 38, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38, 22, 6, 1, 1, 1, 1] 38
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 76
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042127 none CC1=NN(C)C(N2CCOCC2)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 31, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 31, 38, 38, 38, 38] 38
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44])
total number of confs: 90
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042127 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042127
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042127/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042127
Building REAL300000042128
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042128'
/scratch/stefan/7769623/working/building/REAL300000042128 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042128

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042128/0 /scratch/stefan/7769623/working/building/REAL300000042128 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/139
`/scratch/stefan/7769623/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(N3CCOCC3)S2)=C1)

`REAL300000042128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042128 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(N3CCOCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 50, 50, 50, 50, 94, 94, 94, 94, 94, 50, 1, 1, 1, 1, 7, 32, 50, 94, 94, 94, 94, 94, 94, 94, 94, 1] 94
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042128 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(N3CCOCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 84, 38, 38, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 94, 94, 94, 94, 83, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 94] 94
rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 37])
total number of confs: 225
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042128 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(N3CCOCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 50, 50, 50, 50, 30, 7, 1, 11, 11, 11, 11, 11, 12, 11, 11, 50] 94
rigid atoms, others: [10, 11, 12, 13, 14, 15, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042128 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042128
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042128/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042128
Building REAL300000042129
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042129'
/scratch/stefan/7769623/working/building/REAL300000042129 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042129

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042129/0 /scratch/stefan/7769623/working/building/REAL300000042129 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/140
`/scratch/stefan/7769623/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=C1)

`REAL300000042129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042129 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 36, 36, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 12, 36, 45, 45, 45, 45, 45, 44, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042129 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 28, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 45, 45, 45, 45, 28, 11, 4, 1, 1, 1, 1, 1, 45] 45
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 95
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042129 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 25, 6, 6, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 45, 45, 45, 45, 25, 6, 1, 4, 4, 3, 4, 4, 45] 45
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042129 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042129/1 /scratch/stefan/7769623/working/building/REAL300000042129 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/141
`/scratch/stefan/7769623/working/3D/141' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=C1)

`REAL300000042129.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042129/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042129 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 58, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 1, 1, 1, 1, 57, 58, 165, 165, 165, 165, 165, 165, 1] 165
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042129 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [165, 165, 165, 165, 165, 165, 165, 110, 110, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 165, 165, 165, 165, 23, 23, 4, 1, 1, 1, 1, 1, 165] 165
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 282
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042129 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [165, 165, 165, 165, 165, 165, 165, 68, 68, 9, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 165, 165, 165, 165, 9, 9, 1, 4, 4, 3, 4, 4, 165] 165
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042129 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042129
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042129/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042129/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042129
Building REAL300000042130
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042130'
/scratch/stefan/7769623/working/building/REAL300000042130 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042130

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042130/0 /scratch/stefan/7769623/working/building/REAL300000042130 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/142
`/scratch/stefan/7769623/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=C1)

`REAL300000042130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042130 none O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 46, 157, 157, 157, 201, 201, 157, 201, 201, 157, 157, 1, 1, 1, 1, 45, 46, 201, 201, 163, 201, 201, 157, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 518
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042130 none O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 157, 157, 37, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 37, 37, 1, 1, 1, 1, 1, 7, 201] 201
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34])
total number of confs: 359
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042130 none O=C([O-])C1=CC=CC(N=NCC2=NC(C3=CC=CC=C3)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 157, 157, 157, 157, 67, 67, 9, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 157, 157, 157, 157, 8, 8, 7, 7, 1, 7, 7, 1, 157] 201
rigid atoms, others: [33, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042130 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042130/1 /scratch/stefan/7769623/working/building/REAL300000042130 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/143
`/scratch/stefan/7769623/working/3D/143' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=C1)

`REAL300000042130.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042130/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042130 none O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 60, 60, 107, 107, 107, 143, 143, 106, 143, 143, 107, 107, 1, 1, 1, 1, 13, 60, 143, 143, 143, 143, 143, 107, 1] 143
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 412
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042130 none O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 143, 143, 143, 143, 119, 35, 35, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 143, 143, 143, 143, 119, 35, 1, 1, 1, 1, 1, 7, 143] 143
rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34])
total number of confs: 336
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042130 none O=C([O-])C1=CC=CC(NN=CC2=NC(C3=CC=CC=C3)=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [107, 107, 107, 107, 107, 107, 107, 50, 8, 8, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 107, 107, 107, 107, 50, 8, 7, 7, 1, 7, 7, 1, 107] 143
rigid atoms, others: [33, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042130 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042130
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042130/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042130/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042130
Building REAL300000042131
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042131'
/scratch/stefan/7769623/working/building/REAL300000042131 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042131

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042131/0 /scratch/stefan/7769623/working/building/REAL300000042131 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/144
`/scratch/stefan/7769623/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C2OC(C)CC2=C1)

`REAL300000042131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042131 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C2OC(C)CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 9, 9, 28, 54, 54, 53, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 9, 28, 54, 54, 53, 54, 1, 2, 2, 2, 1, 1, 1] 56
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 34, 17, 18, 19, 20, 21, 22, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37])
total number of confs: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042131 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C2OC(C)CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 54, 54, 54, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 54, 54, 54, 54, 54, 54, 56, 56, 56, 54, 40, 10, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54] 56
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042131 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042131
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042131/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042131
Building REAL300000042132
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042132'
/scratch/stefan/7769623/working/building/REAL300000042132 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042132

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042132/0 /scratch/stefan/7769623/working/building/REAL300000042132 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/145
`/scratch/stefan/7769623/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCC3=CC=C(Cl)C=C32)=C1)

`REAL300000042132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042132 none O=C([O-])C1=CC=CC(NN=C2CCCC3=CC=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 35
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042132 none O=C([O-])C1=CC=CC(NN=C2CCCC3=CC=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 20
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 24, 25])
total number of confs: 34
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042132 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042132
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042132/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042132
Building REAL300000042133
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042133'
/scratch/stefan/7769623/working/building/REAL300000042133 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042133

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042133/0 /scratch/stefan/7769623/working/building/REAL300000042133 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/146
`/scratch/stefan/7769623/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC(Cl)=CC=C2N=C1CN=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042133 none CN1C2=CC(Cl)=CC=C2N=C1CN=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 56, 56, 85, 85, 85, 85, 85, 86, 86, 85, 2, 2, 2, 1, 1, 1, 8, 8, 85, 85, 85, 85] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042133 none CN1C2=CC(Cl)=CC=C2N=C1CN=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 86, 86, 86, 85, 85, 85, 43, 43, 1, 1, 1, 1] 86
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042133 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042133/1 /scratch/stefan/7769623/working/building/REAL300000042133 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/147
`/scratch/stefan/7769623/working/3D/147' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC2=CC=C(Cl)C=C21)

`REAL300000042133.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042133/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042133 none CN1C(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC2=CC=C(Cl)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 10, 10, 40, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 40, 58, 58, 58, 58, 1, 1, 1] 58
rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042133 none CN1C(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC2=CC=C(Cl)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [58, 58, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 42, 12, 1, 1, 1, 1, 58, 58, 58] 58
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042133 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042133
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042133/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042133/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042133
Building REAL300000042134
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042134'
/scratch/stefan/7769623/working/building/REAL300000042134 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042134

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042134/0 /scratch/stefan/7769623/working/building/REAL300000042134 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/148
`/scratch/stefan/7769623/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCOCC1)

`REAL300000042134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042134 none COCCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [181, 154, 100, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 120, 120, 120, 120, 112, 181, 181, 181, 148, 154, 108, 108, 48, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 120, 120, 120] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 1013
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042134 none COCCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 37, 22, 8, 1, 8, 42, 42, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 83, 83, 83, 37, 37, 22, 22, 8, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 389
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042134 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042134
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042134/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042134
Building REAL300000042135
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042135'
/scratch/stefan/7769623/working/building/REAL300000042135 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042135

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042135/0 /scratch/stefan/7769623/working/building/REAL300000042135 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/149
`/scratch/stefan/7769623/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C=C2Cl)=C1)

`REAL300000042135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042135 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 53, 53, 104, 104, 59, 104, 104, 104, 176, 201, 201, 177, 196, 201, 201, 201, 1, 1, 1, 1, 11, 53, 104, 104, 104, 104, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([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: 602
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042135 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 140, 54, 54, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 140, 54, 22, 22, 22, 22, 1, 1, 1, 201] 201
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 441
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042135 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 49, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 8, 11, 22, 22, 22, 104, 104, 104, 104, 49, 13, 1, 1, 1, 1, 22, 22, 22, 104] 201
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042135 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042135
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042135/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042135
Building REAL300000042136
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042136'
/scratch/stefan/7769623/working/building/REAL300000042136 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042136

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042136/0 /scratch/stefan/7769623/working/building/REAL300000042136 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/150
`/scratch/stefan/7769623/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)(C)C)C=C1)

`REAL300000042136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042136 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 58, 58, 37, 51, 82, 87, 87, 87, 58, 58, 29, 29, 29, 8, 1, 1, 1, 1, 58, 58, 87, 87, 87, 87, 87, 87, 87, 87, 87, 58, 58] 87
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 269
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042136 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 6, 28, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 3, 7, 7, 7, 1, 1, 6, 6, 6, 28, 58, 58, 58, 58, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 87
rigid atoms, others: [32, 1, 33, 43, 44, 13, 14, 15, 16, 17, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 136
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042136 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042136
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042136/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042136
Building REAL300000042137
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042137'
/scratch/stefan/7769623/working/building/REAL300000042137 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042137

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042137/0 /scratch/stefan/7769623/working/building/REAL300000042137 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/151
`/scratch/stefan/7769623/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC3=C2OCC3)=C1)

`REAL300000042137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042137 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC3=C2OCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 10, 31, 39, 39, 39, 39, 39, 39, 1] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042137 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC3=C2OCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 39, 39, 39, 27, 8, 1, 1, 1, 1, 1, 1, 39] 39
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 21, 22, 23, 24, 25, 26])
total number of confs: 90
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042137 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042137
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042137/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042137
Building REAL300000042138
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042138'
/scratch/stefan/7769623/working/building/REAL300000042138 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042138

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042138/0 /scratch/stefan/7769623/working/building/REAL300000042138 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/152
`/scratch/stefan/7769623/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=CC(Br)=C2)=C1)

`REAL300000042138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042138 none O=C([O-])C1=CC=CC(NN=CC2=CN=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 13, 37, 65, 65, 65, 1] 65
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042138 none O=C([O-])C1=CC=CC(NN=CC2=CN=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 46, 10, 1, 1, 1, 65] 65
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042138 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042138
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042138/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042138
Building REAL300000042139
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042139'
/scratch/stefan/7769623/working/building/REAL300000042139 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042139

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042139/0 /scratch/stefan/7769623/working/building/REAL300000042139 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/153
`/scratch/stefan/7769623/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCOC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042139 none CCCCOC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 24, 51, 51, 51, 51, 51, 51, 51, 51, 83, 83, 83, 79, 79, 66, 66, 31, 31, 1, 1, 1, 1, 4, 24, 51, 51, 51, 51] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 516
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042139 none CCCCOC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 172, 112, 51, 51, 51, 51, 51, 51, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 172, 172, 51, 51, 51, 51, 24, 6, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 653
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042139 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042139
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042139/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042139
Building REAL300000042140
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042140'
/scratch/stefan/7769623/working/building/REAL300000042140 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042140

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042140/0 /scratch/stefan/7769623/working/building/REAL300000042140 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/154
`/scratch/stefan/7769623/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1)

`REAL300000042140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042140 none CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 9, 13, 13, 11, 13, 13, 1, 2, 2, 2, 1, 1, 1, 1, 37, 37, 37, 37, 1, 1, 9, 9, 13, 13, 13, 13, 13, 1, 1] 74
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 46, 15, 16, 17, 18, 25, 47, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 100
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: REAL300000042140 none CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 58, 58, 74, 74, 74, 74, 74, 74, 74, 74, 13, 3, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 74, 74, 74, 74, 13, 13, 3, 3, 1, 1, 1, 1, 1, 13, 13] 74
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47])
total number of confs: 122
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042140 none CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 74, 74, 74, 74, 74, 74, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 37, 37, 74, 74, 74, 74, 74, 74, 74, 37, 37] 74
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 248
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042140 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042140/1 /scratch/stefan/7769623/working/building/REAL300000042140 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/155
`/scratch/stefan/7769623/working/3D/155' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1)

`REAL300000042140.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042140/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042140 none CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 9, 13, 13, 12, 13, 13, 1, 2, 2, 2, 1, 1, 1, 1, 21, 21, 21, 21, 1, 1, 9, 9, 13, 13, 13, 13, 13, 1, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 32, 46, 15, 16, 17, 18, 25, 47, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 73
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: REAL300000042140 none CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 13, 13, 13, 13, 33, 33, 43, 43, 43, 43, 43, 43, 43, 43, 13, 3, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 43, 43, 43, 43, 13, 13, 3, 3, 1, 1, 1, 1, 1, 13, 13] 43
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47])
total number of confs: 85
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042140 none CC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [21, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 43, 43, 43, 43, 43, 43, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 21, 21, 43, 43, 43, 43, 43, 43, 43, 21, 21] 43
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 148
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042140 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042140
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042140/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042140/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042140
Building REAL300000042141
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042141'
/scratch/stefan/7769623/working/building/REAL300000042141 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042141

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042141/0 /scratch/stefan/7769623/working/building/REAL300000042141 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/156
`/scratch/stefan/7769623/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1COCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042141 none CC(CC1COCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 19, 19, 19, 8, 35, 35, 52, 52, 52, 52, 52, 52, 52, 52, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 52, 52, 52, 52] 101
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 39, 34, 35, 36, 38, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042141 none CC(CC1COCCN1C(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [29, 7, 29, 44, 52, 52, 52, 52, 52, 52, 88, 88, 101, 101, 101, 101, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 29, 44, 44, 52, 52, 52, 52, 52, 52, 52, 101, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1] 101
rigid atoms, others: [51, 49, 50, 17, 18, 19, 20, 21, 22, 23, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 350
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042141 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042141
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042141/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042141
Building REAL300000042142
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042142'
/scratch/stefan/7769623/working/building/REAL300000042142 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042142

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042142/0 /scratch/stefan/7769623/working/building/REAL300000042142 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/157
`/scratch/stefan/7769623/working/3D/157' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2CCC(C(F)(F)F)CC2)=C1)

`REAL300000042142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042142 none O=C([O-])C1=CC=CC(N=NCC2CCC(C(F)(F)F)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 61, 61, 58, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 40, 41, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 225
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042142 none O=C([O-])C1=CC=CC(N=NCC2CCC(C(F)(F)F)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 41, 41, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61] 61
rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 37])
total number of confs: 100
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042142 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042142
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042142/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042142
Building REAL300000042143
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042143'
/scratch/stefan/7769623/working/building/REAL300000042143 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042143

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042143/0 /scratch/stefan/7769623/working/building/REAL300000042143 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/158
`/scratch/stefan/7769623/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Br)C=CS2)=C1)

`REAL300000042143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042143 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)C=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 36, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 11, 36, 50, 50, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042143 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)C=CS2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 32, 10, 1, 1, 50] 50
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042143 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042143
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042143/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042143
Building REAL300000042144
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042144'
/scratch/stefan/7769623/working/building/REAL300000042144 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042144

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042144/0 /scratch/stefan/7769623/working/building/REAL300000042144 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/159
`/scratch/stefan/7769623/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=NC=C1F)

`REAL300000042144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042144 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=NC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 93, 93, 93, 93, 93, 93, 93, 51, 51, 51, 10, 1, 1, 1, 1, 93, 93] 93
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 151
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042144 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=NC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [11, 1, 11, 11, 64, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 64, 93, 93, 93, 93, 1, 1] 93
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 203
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042144 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042144
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042144/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042144
Building REAL300000042145
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042145'
/scratch/stefan/7769623/working/building/REAL300000042145 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042145

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042145/0 /scratch/stefan/7769623/working/building/REAL300000042145 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/160
`/scratch/stefan/7769623/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1O)

`REAL300000042145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042145 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 35, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 4, 4, 4, 1, 1, 10, 35, 74, 74, 74, 74, 2] 148
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 150
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042145 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [74, 74, 74, 74, 74, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74, 47, 11, 1, 1, 1, 1, 148] 148
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 264
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042145 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042145
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042145/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042145
Building REAL300000042146
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042146'
/scratch/stefan/7769623/working/building/REAL300000042146 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042146

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042146/0 /scratch/stefan/7769623/working/building/REAL300000042146 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/161
`/scratch/stefan/7769623/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CC=C1[N+](=O)[O-])

`REAL300000042146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042146 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 33, 33, 33, 33, 33, 33, 33, 34, 34, 31, 31, 31, 10, 1, 1, 1, 1, 33, 33, 33] 34
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 71
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042146 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 17, 33, 33, 33, 33, 33, 34, 34, 33, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 17, 33, 33, 33, 33, 1, 1, 1] 34
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 79
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042146 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042146
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042146/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042146
Building REAL300000042147
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042147'
/scratch/stefan/7769623/working/building/REAL300000042147 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042147

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042147/0 /scratch/stefan/7769623/working/building/REAL300000042147 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/162
`/scratch/stefan/7769623/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=C1)

`REAL300000042147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042147 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 69, 70, 70, 70, 151, 201, 201, 201, 201, 70, 70, 70, 1, 1, 1, 1, 7, 25, 70, 70, 201, 201, 70, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 476
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042147 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC(F)(F)F)C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 31, 7, 7, 1, 1, 1, 1, 1, 1, 11, 34, 34, 34, 34, 1, 1, 1, 70, 70, 70, 70, 31, 7, 1, 1, 34, 34, 1, 70] 201
rigid atoms, others: [34, 10, 11, 12, 13, 14, 15, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 35])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042147 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042147
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042147/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042147
Building REAL300000042148
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042148'
/scratch/stefan/7769623/working/building/REAL300000042148 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042148

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042148/0 /scratch/stefan/7769623/working/building/REAL300000042148 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/163
`/scratch/stefan/7769623/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F)

`REAL300000042148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042148 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [76, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 104, 104, 104, 104, 104, 104, 104, 77, 77, 77, 76, 76, 8, 1, 1, 1, 1, 104, 104, 104] 120
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 340
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042148 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [31, 13, 1, 13, 13, 62, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 62, 104, 104, 104, 104, 1, 1, 1] 120
rigid atoms, others: [32, 33, 2, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 309
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042148 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042148
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042148/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042148
Building REAL300000042149
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042149'
/scratch/stefan/7769623/working/building/REAL300000042149 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042149

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042149/0 /scratch/stefan/7769623/working/building/REAL300000042149 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/164
`/scratch/stefan/7769623/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=C1)

`REAL300000042149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042149 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 28, 28, 25, 28, 28, 28, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 28, 28, 28, 28, 1] 28
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 77
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042149 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 17, 17, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 28] 28
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 45
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042149 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 25] 28
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38])
total number of confs: 40
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042149 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042149
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042149/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042149
Building REAL300000042150
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042150'
/scratch/stefan/7769623/working/building/REAL300000042150 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042150

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042150/0 /scratch/stefan/7769623/working/building/REAL300000042150 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/165
`/scratch/stefan/7769623/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)OCO2)

`REAL300000042150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042150 none COC1=CC2=C(C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)OCO2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 44, 82, 82, 82, 82, 82, 83, 83, 82, 1, 1, 1, 4, 4, 4, 1, 1, 11, 44, 82, 82, 82, 82, 1, 1] 83
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042150 none COC1=CC2=C(C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)OCO2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 82, 82, 82, 82, 82, 82, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 82, 82, 83, 83, 83, 82, 82, 53, 12, 1, 1, 1, 1, 82, 82] 83
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042150 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042150
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042150/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042150
Building REAL300000042151
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042151'
/scratch/stefan/7769623/working/building/REAL300000042151 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042151

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042151/0 /scratch/stefan/7769623/working/building/REAL300000042151 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/166
`/scratch/stefan/7769623/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(Cl)C=C2F)S1)

`REAL300000042151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042151 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(Cl)C=C2F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 108, 108, 108, 108, 201, 201, 176, 200, 201, 201, 201, 108, 39, 39, 39, 8, 1, 1, 1, 1, 108, 108, 201, 201, 201] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 419
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: REAL300000042151 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(Cl)C=C2F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 73, 73, 173, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 73, 73, 73, 177, 201, 201, 201, 201, 13, 13, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 492
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042151 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(Cl)C=C2F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 12, 12, 52, 108, 109, 109, 108, 108, 109, 109, 108, 1, 1, 1, 1, 1, 13, 13, 1, 12, 13, 13, 13, 1, 13, 13, 13, 52, 109, 109, 109, 108, 1, 1, 13, 13, 13] 201
rigid atoms, others: [1, 34, 35, 13, 14, 15, 16, 17, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 264
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042151 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042151
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042151/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042151
Building REAL300000042152
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042152'
/scratch/stefan/7769623/working/building/REAL300000042152 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042152

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042152/0 /scratch/stefan/7769623/working/building/REAL300000042152 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/167
`/scratch/stefan/7769623/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(F)C=C2F)=C1)

`REAL300000042152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042152 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 43, 141, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 42, 43, 141, 141, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042152 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 147, 147, 47, 47, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 47, 47, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 349
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042152 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042152
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042152/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042152
Building REAL300000042153
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042153'
/scratch/stefan/7769623/working/building/REAL300000042153 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042153

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042153/0 /scratch/stefan/7769623/working/building/REAL300000042153 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/168
`/scratch/stefan/7769623/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCOC3=CC(F)=CC=C32)=C1)

`REAL300000042153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042153 none O=C([O-])C1=CC=CC(NN=C2CCCOC3=CC(F)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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
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, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042153 none O=C([O-])C1=CC=CC(NN=C2CCCOC3=CC(F)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 36])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042153 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042153
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042153/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042153
Building REAL300000042154
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042154'
/scratch/stefan/7769623/working/building/REAL300000042154 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042154

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042154/0 /scratch/stefan/7769623/working/building/REAL300000042154 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/169
`/scratch/stefan/7769623/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042154 none COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 10, 10, 41, 114, 114, 114, 114, 114, 115, 115, 114, 3, 3, 3, 1, 3, 3, 1, 3, 3, 1, 1, 10, 41, 114, 114, 114, 114] 135
rigid atoms, others: [1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 29] set([0, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 216
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: REAL300000042154 none COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [134, 114, 114, 114, 74, 114, 135, 135, 114, 135, 135, 114, 114, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 134, 134, 134, 114, 135, 135, 114, 135, 135, 114, 114, 63, 12, 1, 1, 1, 1] 135
rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 490
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042154 none COC1=CC(C2=CC=CC=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 21, 21, 74, 135, 135, 135, 135, 135, 135, 135, 135, 7, 7, 7, 3, 1, 1, 1, 1, 1, 3, 3, 21, 74, 135, 135, 135, 135] 135
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 270
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042154 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042154
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042154/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042154
Building REAL300000042155
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042155'
/scratch/stefan/7769623/working/building/REAL300000042155 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042155

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042155/0 /scratch/stefan/7769623/working/building/REAL300000042155 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/170
`/scratch/stefan/7769623/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=C1)

`REAL300000042155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042155 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35, 35, 45, 45, 45, 45, 45, 45, 35, 1, 1, 1, 1, 35, 35, 35, 35, 45, 45, 45, 45, 35, 35, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 95
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: REAL300000042155 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 27, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 45, 45, 45, 45, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 45] 45
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 70
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042155 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Cl)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 35, 35, 35, 35, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 35] 45
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 32, 35])
total number of confs: 50
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042155 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042155
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042155/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042155
Building REAL300000042156
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042156'
/scratch/stefan/7769623/working/building/REAL300000042156 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042156

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042156/0 /scratch/stefan/7769623/working/building/REAL300000042156 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/171
`/scratch/stefan/7769623/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OCCC(=O)[O-])

`REAL300000042156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042156 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 26, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 9, 36, 41, 57, 53, 4, 4, 4, 1, 7, 26, 51, 51, 51, 51, 1, 1, 36, 36, 40, 40] 201
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 36, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 311
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042156 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 51, 51, 15, 15, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 51, 50, 50, 138, 185, 189, 201, 197, 89, 89, 89, 51, 15, 3, 1, 1, 1, 1, 51, 51, 185, 185, 189, 189] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 576
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042156 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042156
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042156/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042156
Building REAL300000042157
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042157'
/scratch/stefan/7769623/working/building/REAL300000042157 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042157

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042157/0 /scratch/stefan/7769623/working/building/REAL300000042157 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/172
`/scratch/stefan/7769623/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OCC2=CC=CC=C2)CCO1)

`REAL300000042157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042157 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OCC2=CC=CC=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 49, 49, 49, 59, 59, 85, 201, 201, 201, 201, 201, 201, 49, 49, 49, 29, 29, 29, 29, 1, 1, 1, 1, 49, 49, 49, 201, 201, 201, 201, 201, 201, 201, 49, 49, 49, 49] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35, 36] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 720
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042157 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OCC2=CC=CC=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 44, 80, 175, 175, 201, 201, 201, 201, 201, 201, 201, 201, 44, 44, 34, 18, 34, 3, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 81, 81, 81, 80, 201, 201, 201, 201, 44, 44, 44, 3, 3, 1, 1, 1, 1, 1, 44, 44, 44, 44] 201
rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49, 50])
total number of confs: 486
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042157 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OCC2=CC=CC=C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 2, 2, 4, 23, 44, 44, 23, 44, 44, 1, 1, 1, 5, 5, 5, 4, 49, 49, 49, 49, 1, 1, 1, 23, 23, 44, 44, 23, 44, 44, 1, 1, 1, 1] 201
rigid atoms, others: [1, 48, 37, 38, 39, 47, 13, 14, 15, 16, 49, 50, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042157 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042157
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042157/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042157
Building REAL300000042158
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042158'
/scratch/stefan/7769623/working/building/REAL300000042158 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042158

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042158/0 /scratch/stefan/7769623/working/building/REAL300000042158 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/173
`/scratch/stefan/7769623/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CCCCCC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042158 none CC(C)(C)OC(=O)NC1CCCCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [26, 22, 26, 26, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 45, 45, 45, 45, 45, 45, 45, 45, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 115
rigid atoms, others: [45, 43, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 47, 46, 41, 39, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 48, 49, 50, 51])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042158 none CC(C)(C)OC(=O)NC1CCCCCC1N=NC1=CC=CC(C(=O)[O-])=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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 115, 102, 80, 102, 45, 45, 45, 45, 45, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 115, 80, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1] 115
rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 326
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042158 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042158
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042158/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042158
Building REAL300000042159
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042159'
/scratch/stefan/7769623/working/building/REAL300000042159 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042159

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042159/0 /scratch/stefan/7769623/working/building/REAL300000042159 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/174
`/scratch/stefan/7769623/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=NNC2=CC=CC=C21)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042159 none CC(CCC1=NNC2=CC=CC=C21)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 39, 39, 39, 39, 10, 10, 5, 5, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40])
total number of confs: 408
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042159 none CC(CCC1=NNC2=CC=CC=C21)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 44, 91, 114, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 44, 97, 97, 114, 109, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 615
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042159 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042159
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042159/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042159
Building REAL300000042160
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042160'
/scratch/stefan/7769623/working/building/REAL300000042160 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042160

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042160/0 /scratch/stefan/7769623/working/building/REAL300000042160 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/175
`/scratch/stefan/7769623/working/3D/175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC(F)F)C=C2)=C1)

`REAL300000042160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042160 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 55, 55, 39, 55, 178, 201, 201, 55, 55, 1, 1, 1, 1, 9, 39, 55, 55, 201, 55, 55, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 450
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042160 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 5, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 23, 3, 3, 1, 1, 1, 1, 1, 1, 12, 43, 43, 1, 1, 55, 55, 55, 55, 23, 3, 1, 1, 43, 1, 1, 55] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042160 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042160
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042160/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042160
Building REAL300000042161
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042161'
/scratch/stefan/7769623/working/building/REAL300000042161 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042161

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042161/0 /scratch/stefan/7769623/working/building/REAL300000042161 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/176
`/scratch/stefan/7769623/working/3D/176' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Cl)C=CC3=CC=CN=C32)=C1)

`REAL300000042161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042161 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)C=CC3=CC=CN=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 11, 35, 92, 92, 92, 92, 92, 1] 92
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042161 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)C=CC3=CC=CN=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 92, 92, 92, 92, 58, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 58, 12, 1, 1, 1, 1, 1, 92] 92
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042161 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042161
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042161/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042161
Building REAL300000042162
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042162'
/scratch/stefan/7769623/working/building/REAL300000042162 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042162

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042162/0 /scratch/stefan/7769623/working/building/REAL300000042162 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/177
`/scratch/stefan/7769623/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1)

`REAL300000042162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042162 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 25, 18, 18, 18, 18, 1, 1, 1, 1, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 35, 25, 25] 35
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 136
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: REAL300000042162 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 15, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 15, 35, 35, 35, 35, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 8, 8] 35
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47])
total number of confs: 91
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042162 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 5, 8, 8, 5, 8, 8, 1, 3, 3, 3, 3, 25, 25, 25, 25, 1, 1, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 1, 1] 35
rigid atoms, others: [1, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 46, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 69
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042162 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042162/1 /scratch/stefan/7769623/working/building/REAL300000042162 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/178
`/scratch/stefan/7769623/working/3D/178' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1)

`REAL300000042162.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042162/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042162 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 25, 25, 25, 25, 25, 40, 40, 40, 40, 40, 40, 25, 20, 20, 20, 20, 1, 1, 1, 1, 25, 25, 25, 25, 25, 40, 40, 40, 40, 40, 40, 40, 25, 25] 40
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 170
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: REAL300000042162 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 16, 33, 33, 40, 40, 40, 40, 40, 40, 40, 40, 10, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 40, 40, 40, 40, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 10, 10] 40
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47])
total number of confs: 104
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042162 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 4, 4, 4, 4, 25, 25, 25, 25, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 1, 1] 40
rigid atoms, others: [1, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 46, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 68
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042162 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042162
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042162/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042162/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042162
Building REAL300000042163
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042163'
/scratch/stefan/7769623/working/building/REAL300000042163 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042163

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042163/0 /scratch/stefan/7769623/working/building/REAL300000042163 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/179
`/scratch/stefan/7769623/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21)

`REAL300000042163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042163 none CC(C)(C)OC(=O)NC1CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [35, 29, 35, 35, 11, 6, 11, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 1, 6, 22, 22, 22, 22, 1, 1, 1, 1] 120
rigid atoms, others: [11, 49, 38, 7, 8, 9, 10, 39, 12, 46, 47, 48, 40, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45])
total number of confs: 127
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042163 none CC(C)(C)OC(=O)NC1CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 120, 120, 93, 64, 93, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 22, 22, 120, 120, 120, 120, 120, 120, 120, 120, 120, 64, 22, 22, 22, 8, 1, 1, 1, 1, 22, 22, 22, 22] 120
rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49])
total number of confs: 325
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042163 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042163
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042163/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042163
Building REAL300000042164
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042164'
/scratch/stefan/7769623/working/building/REAL300000042164 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042164

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042164/0 /scratch/stefan/7769623/working/building/REAL300000042164 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/180
`/scratch/stefan/7769623/working/3D/180' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Cl)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O)

`REAL300000042164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042164 none COC1=CC(Cl)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 4, 4, 4, 1, 1, 10, 35, 76, 76, 76, 76, 2] 152
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 155
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042164 none COC1=CC(Cl)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 53, 53, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 76, 76, 76, 76, 76, 76, 76, 53, 9, 1, 1, 1, 1, 152] 152
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 266
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042164 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042164
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042164/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042164
Building REAL300000042165
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042165'
/scratch/stefan/7769623/working/building/REAL300000042165 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042165

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042165/0 /scratch/stefan/7769623/working/building/REAL300000042165 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/181
`/scratch/stefan/7769623/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2NC3=C(CC(N=NC4=CC=CC(C(=O)[O-])=C4)CC3)C2=C1)

`REAL300000042165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042165 none COC1=CC=C2NC3=C(CC(N=NC4=CC=CC(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 1, 1, 1, 1, 1] 28
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43] set([0, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042165 none COC1=CC=C2NC3=C(CC(N=NC4=CC=CC(C(=O)[O-])=C4)CC3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 28, 28, 28, 28, 28] 28
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43])
total number of confs: 65
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042165 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042165
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042165/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042165
Building REAL300000042166
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042166'
/scratch/stefan/7769623/working/building/REAL300000042166 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042166

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042166/0 /scratch/stefan/7769623/working/building/REAL300000042166 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/182
`/scratch/stefan/7769623/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1[O-])

`REAL300000042166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042166 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 1, 1, 1, 1, 23, 23] 23
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 42
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042166 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 15, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 23, 23, 23, 23, 1, 1] 23
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 49
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042166 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042166/1 /scratch/stefan/7769623/working/building/REAL300000042166 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/183
`/scratch/stefan/7769623/working/3D/183' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1O)

`REAL300000042166.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042166/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042166 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 69, 69, 69, 69, 69, 69, 69, 69, 41, 41, 41, 10, 1, 1, 1, 1, 69, 69, 138] 138
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 258
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042166 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(F)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 45, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 45, 69, 69, 69, 69, 1, 1, 2] 138
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 155
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042166 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042166
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042166/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042166/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042166
Building REAL300000042167
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042167'
/scratch/stefan/7769623/working/building/REAL300000042167 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042167

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042167/0 /scratch/stefan/7769623/working/building/REAL300000042167 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/184
`/scratch/stefan/7769623/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC3=C2OCC3)=C1)

`REAL300000042167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042167 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC3=C2OCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 9, 31, 41, 41, 41, 41, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042167 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC3=C2OCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 41, 41, 41, 27, 8, 1, 1, 1, 1, 1, 1, 41] 41
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 21, 22, 23, 24, 25, 26])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042167 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042167
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042167/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042167
Building REAL300000042168
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042168'
/scratch/stefan/7769623/working/building/REAL300000042168 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042168

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042168/0 /scratch/stefan/7769623/working/building/REAL300000042168 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/185
`/scratch/stefan/7769623/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1)

`REAL300000042168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042168 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 16, 16, 14, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 4, 14, 16, 16, 16, 1] 16
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 36
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042168 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 8, 1, 1, 1, 16] 16
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042168 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042168
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042168/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042168
Building REAL300000042169
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042169'
/scratch/stefan/7769623/working/building/REAL300000042169 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042169

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042169/0 /scratch/stefan/7769623/working/building/REAL300000042169 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/186
`/scratch/stefan/7769623/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=CN2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CN=C12)

`REAL300000042169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042169 none CC1=CC(Br)=CN2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 61, 87, 87, 87, 87, 87, 88, 88, 87, 1, 1, 1, 2, 2, 2, 1, 1, 10, 61, 87, 87, 87, 87, 1] 88
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042169 none CC1=CC(Br)=CN2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [87, 87, 87, 87, 87, 87, 87, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 87, 87, 88, 88, 88, 87, 87, 44, 12, 1, 1, 1, 1, 87] 88
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042169 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042169
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042169/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042169
Building REAL300000042170
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042170'
/scratch/stefan/7769623/working/building/REAL300000042170 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042170

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042170/0 /scratch/stefan/7769623/working/building/REAL300000042170 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/187
`/scratch/stefan/7769623/working/3D/187' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=C1)

`REAL300000042170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042170 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 59, 59, 59, 132, 201, 201, 201, 201, 201, 59, 59, 1, 1, 1, 1, 26, 27, 59, 132, 132, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([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: 607
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042170 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 163, 163, 58, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 58, 58, 23, 7, 7, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 415
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042170 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3=CC=CN=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 35, 35, 6, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 1, 1, 59, 59, 59, 59, 6, 6, 1, 7, 7, 23, 23, 23, 23, 59] 201
rigid atoms, others: [10, 11, 12, 13, 14, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042170 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042170/1 /scratch/stefan/7769623/working/building/REAL300000042170 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/188
`/scratch/stefan/7769623/working/3D/188' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=C1)

`REAL300000042170.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042170/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042170 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 47, 47, 47, 133, 201, 201, 201, 201, 201, 47, 47, 1, 1, 1, 1, 9, 33, 47, 133, 133, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([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: 555
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042170 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 153, 50, 50, 32, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 201, 153, 50, 32, 7, 7, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 469
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042170 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=CN=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 18, 4, 4, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 32, 1, 1, 47, 47, 47, 47, 18, 4, 1, 9, 9, 32, 32, 32, 32, 47] 201
rigid atoms, others: [10, 11, 12, 13, 14, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042170 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042170
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042170/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042170/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042170
Building REAL300000042171
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042171'
/scratch/stefan/7769623/working/building/REAL300000042171 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042171

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042171/0 /scratch/stefan/7769623/working/building/REAL300000042171 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/189
`/scratch/stefan/7769623/working/3D/189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2CCC(=O)NC3=CC=CC=C32)=CC=C1)

`REAL300000042171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042171 none O=C([O-])C1=CC(NN=C2CCC(=O)NC3=CC=CC=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1] 20
rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042171 none O=C([O-])C1=CC(NN=C2CCC(=O)NC3=CC=CC=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 19, 20, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19] 20
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23, 24, 36])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042171 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042171
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042171/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042171
Building REAL300000042172
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042172'
/scratch/stefan/7769623/working/building/REAL300000042172 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042172

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042172/0 /scratch/stefan/7769623/working/building/REAL300000042172 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/190
`/scratch/stefan/7769623/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CN=C12)

`REAL300000042172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042172 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 49, 70, 70, 70, 70, 70, 71, 71, 70, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 49, 70, 70, 70, 70, 1, 1, 1, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 36, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042172 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 70, 70, 70, 70, 70, 71, 71, 71, 70, 42, 12, 1, 1, 1, 1, 70, 70, 70, 70] 71
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042172 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042172
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042172/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042172
Building REAL300000042173
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042173'
/scratch/stefan/7769623/working/building/REAL300000042173 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042173

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042173/0 /scratch/stefan/7769623/working/building/REAL300000042173 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/191
`/scratch/stefan/7769623/working/3D/191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(F)=CC=C2N1)

`REAL300000042173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042173 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(F)=CC=C2N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 12, 12, 62, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 62, 90, 90, 90, 90, 1, 1, 1, 1] 90
rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042173 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(F)=CC=C2N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 40, 10, 1, 1, 1, 1, 90, 90, 90, 90] 90
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042173 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042173
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042173/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042173
Building REAL300000042174
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042174'
/scratch/stefan/7769623/working/building/REAL300000042174 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042174

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042174/0 /scratch/stefan/7769623/working/building/REAL300000042174 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/192
`/scratch/stefan/7769623/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042174 none COC(=O)COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 12, 58, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 44, 44, 44, 44, 44, 45, 45, 44, 1, 1, 59, 59, 59, 12, 12, 1, 1, 6, 23, 44, 44, 44, 44, 1, 1] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 23, 38, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 248
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042174 none COC(=O)COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 83, 45, 33, 45, 44, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 45, 201, 201, 201, 135, 135, 45, 44, 17, 4, 1, 1, 1, 1, 44, 45] 201
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 695
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042174 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042174
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042174/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042174
Building REAL300000042175
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042175'
/scratch/stefan/7769623/working/building/REAL300000042175 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042175

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042175/0 /scratch/stefan/7769623/working/building/REAL300000042175 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/193
`/scratch/stefan/7769623/working/3D/193' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042175 none CC(=O)NC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 62, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1, 3, 3, 3, 3, 1, 1, 13, 13, 13, 62, 118, 118, 118, 118, 1, 1] 125
rigid atoms, others: [3, 4, 5, 6, 7, 8, 38, 21, 22, 27, 28, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 249
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042175 none CC(=O)NC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 118, 98, 118, 118, 53, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 118, 118, 125, 125, 125, 125, 118, 118, 54, 54, 54, 12, 1, 1, 1, 1, 118, 118] 125
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 300
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042175 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042175
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042175/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042175
Building REAL300000042176
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042176'
/scratch/stefan/7769623/working/building/REAL300000042176 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042176

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042176/0 /scratch/stefan/7769623/working/building/REAL300000042176 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/194
`/scratch/stefan/7769623/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=C1)

`REAL300000042176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042176 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 46, 46, 79, 79, 79, 79, 201, 201, 79, 201, 201, 201, 201, 201, 201, 79, 1, 1, 1, 1, 10, 46, 79, 79, 201, 201, 115, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([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: 571
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042176 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 156, 52, 52, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 156, 52, 13, 13, 1, 1, 1, 1, 201] 201
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 458
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042176 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(F)(F)F)=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 40, 9, 9, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 13, 13, 13, 1, 79, 79, 79, 79, 40, 9, 1, 1, 13, 13, 1, 13, 79] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042176 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042176
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042176/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042176
Building REAL300000042177
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042177'
/scratch/stefan/7769623/working/building/REAL300000042177 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042177

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042177/0 /scratch/stefan/7769623/working/building/REAL300000042177 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/195
`/scratch/stefan/7769623/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=C1)

`REAL300000042177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042177 none O=C([O-])C1=CC=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 70, 70, 175, 175, 175, 175, 175, 180, 180, 180, 180, 180, 1, 1, 1, 1, 13, 70, 175, 175, 180, 180, 180, 180, 180, 1] 180
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 252
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: REAL300000042177 none O=C([O-])C1=CC=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [180, 180, 180, 180, 180, 180, 180, 130, 35, 35, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 130, 35, 6, 6, 1, 1, 1, 1, 1, 180] 180
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 402
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042177 none O=C([O-])C1=CC=CC(NN=CC2=NNC=C2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 78, 13, 13, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 175, 175, 175, 175, 78, 13, 1, 1, 6, 6, 2, 6, 6, 175] 180
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 337
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042177 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042177/1 /scratch/stefan/7769623/working/building/REAL300000042177 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/196
`/scratch/stefan/7769623/working/3D/196' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NNC=C2C2=CC=CC=C2)=C1)

`REAL300000042177.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042177/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042177 none O=C([O-])C1=CC=CC(N=NCC2=NNC=C2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 9, 9, 66, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 1, 1, 1, 1, 66, 65, 181, 181, 181, 181, 181, 181, 181, 1] 181
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 363
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042177 none O=C([O-])C1=CC=CC(N=NCC2=NNC=C2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 181, 181, 125, 125, 24, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 24, 24, 6, 6, 1, 1, 1, 1, 1, 181] 181
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 305
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042177 none O=C([O-])C1=CC=CC(N=NCC2=NNC=C2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 180, 181, 181, 64, 64, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 181, 180, 181, 181, 8, 8, 1, 1, 6, 6, 1, 6, 6, 181] 181
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 275
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042177 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042177
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042177/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042177/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042177
Building REAL300000042178
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042178'
/scratch/stefan/7769623/working/building/REAL300000042178 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042178

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042178/0 /scratch/stefan/7769623/working/building/REAL300000042178 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/197
`/scratch/stefan/7769623/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CN1CC2=CC=CC=C2C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042178 none CC(CN1CC2=CC=CC=C2C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 85, 85, 118, 118, 118, 118, 118, 118, 118, 118, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118] 118
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 35, 36, 29, 30, 31] set([0, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40])
total number of confs: 220
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042178 none CC(CN1CC2=CC=CC=C2C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [56, 8, 56, 110, 118, 118, 118, 118, 118, 118, 118, 118, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 56, 56, 56, 56, 110, 110, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1, 1, 1] 118
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 437
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042178 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042178/1 /scratch/stefan/7769623/working/building/REAL300000042178 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/198
`/scratch/stefan/7769623/working/3D/198' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C[NH+]1CC2=CC=CC=C2C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042178.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042178/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042178 none CC(C[NH+]1CC2=CC=CC=C2C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 57, 57, 73, 73, 73, 73, 73, 73, 73, 73, 19, 19, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73] 73
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 36, 37, 30, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41])
total number of confs: 156
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042178 none CC(C[NH+]1CC2=CC=CC=C2C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [36, 8, 36, 68, 73, 73, 73, 73, 73, 73, 73, 73, 73, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 36, 68, 68, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1] 73
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 285
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042178 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042178
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042178/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042178/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042178
Building REAL300000042179
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042179'
/scratch/stefan/7769623/working/building/REAL300000042179 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042179

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042179/0 /scratch/stefan/7769623/working/building/REAL300000042179 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/199
`/scratch/stefan/7769623/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042179 none CN(C)C1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 33, 33, 34, 34, 33, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 33, 33, 33, 33] 34
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 33, 30, 31] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042179 none CN(C)C1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 33, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 34, 34, 34, 33, 33, 33, 33, 11, 1, 1, 1, 1] 34
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 62
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042179 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042179
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042179/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042179
Building REAL300000042180
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042180'
/scratch/stefan/7769623/working/building/REAL300000042180 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042180

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042180/0 /scratch/stefan/7769623/working/building/REAL300000042180 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/200
`/scratch/stefan/7769623/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C2C(=C1)N(C)C(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042180 none CN(C)C1=CC=C2C(=C1)N(C)C(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 34, 34, 34, 34, 35, 35, 34, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 7, 34, 34, 34, 34] 35
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 33, 31] set([0, 2, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 68
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042180 none CN(C)C1=CC=C2C(=C1)N(C)C(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 34, 35, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 35, 35, 35, 35, 34, 34, 34, 35, 35, 35, 11, 1, 1, 1, 1] 35
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 69
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042180 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042180
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042180/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042180
Building REAL300000042181
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042181'
/scratch/stefan/7769623/working/building/REAL300000042181 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042181

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042181/0 /scratch/stefan/7769623/working/building/REAL300000042181 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/201
`/scratch/stefan/7769623/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)F)S2)=C1)

`REAL300000042181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042181 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 11, 37, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042181 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 43, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 54, 54, 54, 54, 42, 7, 1, 1, 54] 54
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 124
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042181 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042181
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042181/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042181
Building REAL300000042182
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042182'
/scratch/stefan/7769623/working/building/REAL300000042182 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042182

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042182/0 /scratch/stefan/7769623/working/building/REAL300000042182 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/202
`/scratch/stefan/7769623/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(Cl)=CC(Cl)=C23)=C1)

`REAL300000042182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042182 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(Cl)=CC(Cl)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 40, 40, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 12, 40, 54, 54, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042182 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(Cl)=CC(Cl)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 38, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 38, 10, 1, 1, 1, 1, 54] 54
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 24, 25, 26, 27])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042182 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042182
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042182/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042182
Building REAL300000042183
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042183'
/scratch/stefan/7769623/working/building/REAL300000042183 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042183

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042183/0 /scratch/stefan/7769623/working/building/REAL300000042183 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/203
`/scratch/stefan/7769623/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=C1)

`REAL300000042183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042183 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 59, 59, 106, 106, 106, 106, 201, 201, 201, 201, 201, 201, 189, 106, 1, 1, 1, 1, 13, 59, 106, 106, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042183 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 199, 163, 53, 53, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 163, 53, 13, 13, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 482
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042183 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC(F)=C3F)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [106, 106, 106, 106, 106, 106, 106, 46, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 13, 13, 1, 106, 106, 106, 106, 46, 6, 1, 1, 13, 13, 13, 106] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042183 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042183
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042183/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042183
Building REAL300000042184
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042184'
/scratch/stefan/7769623/working/building/REAL300000042184 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042184

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042184/0 /scratch/stefan/7769623/working/building/REAL300000042184 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/204
`/scratch/stefan/7769623/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CN2C(=O)C3=CC=CC=C3C2=O)C2=CC=CC=C2)=C1)

`REAL300000042184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042184 none O=C([O-])C1=CC=CC(NN=C(CN2C(=O)C3=CC=CC=C3C2=O)C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 58, 58, 30, 58, 58, 1, 1, 1, 1, 9, 195, 195, 201, 201, 201, 201, 58, 58, 30, 58, 58, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 32, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042184 none O=C([O-])C1=CC=CC(NN=C(CN2C(=O)C3=CC=CC=C3C2=O)C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 20, 4, 4, 1, 4, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 20, 30, 30, 50, 50, 50, 50, 1, 1, 1, 1, 1, 58] 201
rigid atoms, others: [40, 41, 10, 43, 44, 23, 24, 25, 26, 27, 28, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45])
total number of confs: 224
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042184 none O=C([O-])C1=CC=CC(NN=C(CN2C(=O)C3=CC=CC=C3C2=O)C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 138, 32, 32, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 55, 55, 32, 55, 55, 201, 201, 201, 201, 138, 5, 5, 1, 1, 1, 1, 55, 55, 31, 55, 55, 201] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 543
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042184 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042184
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042184/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042184
Building REAL300000042185
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042185'
/scratch/stefan/7769623/working/building/REAL300000042185 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042185

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042185/0 /scratch/stefan/7769623/working/building/REAL300000042185 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/205
`/scratch/stefan/7769623/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1)

`REAL300000042185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042185 none CC(C)(C)OC(=O)NCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 190, 162, 190, 90, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 26, 26, 17, 26, 26, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 90, 90, 4, 1, 1, 1, 1, 26, 26, 17, 26, 26] 201
rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48])
total number of confs: 698
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042185 none CC(C)(C)OC(=O)NCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=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.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 131, 99, 131, 31, 4, 1, 4, 4, 10, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 146, 146, 146, 99, 31, 31, 10, 26, 26, 26, 26, 1, 1, 1, 1, 1] 201
rigid atoms, others: [9, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 489
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042185 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042185
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042185/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042185
Building REAL300000042186
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042186'
/scratch/stefan/7769623/working/building/REAL300000042186 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042186

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042186/0 /scratch/stefan/7769623/working/building/REAL300000042186 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/206
`/scratch/stefan/7769623/working/3D/206' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)OC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21)

`REAL300000042186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042186 none CN1C(=O)OC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 8, 8, 48, 68, 68, 68, 68, 68, 69, 69, 68, 1, 1, 1, 2, 2, 2, 1, 8, 48, 68, 68, 68, 68, 1, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 20, 21, 22, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042186 none CN1C(=O)OC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [68, 68, 68, 68, 68, 68, 68, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 68, 68, 69, 69, 69, 68, 40, 12, 1, 1, 1, 1, 68, 68] 69
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042186 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042186
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042186/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042186
Building REAL300000042187
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042187'
/scratch/stefan/7769623/working/building/REAL300000042187 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042187

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042187/0 /scratch/stefan/7769623/working/building/REAL300000042187 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/207
`/scratch/stefan/7769623/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CN1CC2=CC=CC=C2C1=O)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042187 none CC(CN1CC2=CC=CC=C2C1=O)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 141, 141, 195, 195, 195, 195, 195, 195, 195, 195, 33, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195] 195
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 35, 30, 31] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39])
total number of confs: 373
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042187 none CC(CN1CC2=CC=CC=C2C1=O)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [49, 8, 49, 142, 195, 195, 195, 195, 195, 195, 195, 195, 195, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 142, 142, 195, 195, 195, 195, 195, 195, 1, 1, 1, 1] 195
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 627
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042187 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042187
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042187/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042187
Building REAL300000042188
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042188'
/scratch/stefan/7769623/working/building/REAL300000042188 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042188

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042188/0 /scratch/stefan/7769623/working/building/REAL300000042188 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/208
`/scratch/stefan/7769623/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C2)

`REAL300000042188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042188 none COC1=CC=CC2=C1CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 1, 1] 27
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39] set([0, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042188 none COC1=CC=CC2=C1CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 27, 27, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 27, 27] 27
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042188 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042188
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042188/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042188
Building REAL300000042189
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042189'
/scratch/stefan/7769623/working/building/REAL300000042189 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042189

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042189/0 /scratch/stefan/7769623/working/building/REAL300000042189 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/209
`/scratch/stefan/7769623/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3OCCO3)S2)=C1)

`REAL300000042189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042189 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 55, 55, 102, 102, 102, 102, 201, 201, 201, 201, 102, 1, 1, 1, 1, 13, 55, 102, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 458
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042189 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 164, 51, 51, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 164, 51, 12, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 33])
total number of confs: 463
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042189 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 102, 101, 102, 102, 39, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 102, 101, 102, 102, 39, 6, 1, 12, 12, 13, 12, 13, 102] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042189 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042189
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042189/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042189
Building REAL300000042190
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042190'
/scratch/stefan/7769623/working/building/REAL300000042190 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042190

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042190/0 /scratch/stefan/7769623/working/building/REAL300000042190 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/210
`/scratch/stefan/7769623/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=C1)

`REAL300000042190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042190 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 49, 49, 145, 145, 145, 82, 145, 145, 190, 190, 190, 190, 145, 145, 1, 1, 1, 1, 11, 49, 145, 98, 190, 190, 190, 190, 190, 1] 190
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 542
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042190 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [190, 190, 190, 190, 190, 190, 190, 138, 45, 45, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 190, 190, 190, 190, 138, 45, 6, 6, 1, 1, 1, 1, 1, 190] 190
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])
total number of confs: 441
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042190 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(C3OCCO3)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 5, 12, 5, 5, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [145, 145, 145, 145, 145, 145, 145, 75, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 145, 145, 145, 145, 75, 11, 1, 1, 6, 6, 6, 6, 6, 145] 190
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37])
total number of confs: 288
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042190 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042190
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042190/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042190
Building REAL300000042191
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042191'
/scratch/stefan/7769623/working/building/REAL300000042191 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042191

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042191/0 /scratch/stefan/7769623/working/building/REAL300000042191 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/211
`/scratch/stefan/7769623/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC3=CC=C(F)C=C3S2)=C1)

`REAL300000042191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042191 none O=C([O-])C1=CC=CC(N=NCC2=NC3=CC=C(F)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 127, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 47, 46, 127, 127, 127, 1] 127
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042191 none O=C([O-])C1=CC=CC(N=NCC2=NC3=CC=C(F)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 127, 127, 127, 127, 127, 127, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 8, 8, 1, 1, 1, 127] 127
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042191 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042191/1 /scratch/stefan/7769623/working/building/REAL300000042191 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/212
`/scratch/stefan/7769623/working/3D/212' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC3=CC=C(F)C=C3S2)=C1)

`REAL300000042191.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042191/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042191 none O=C([O-])C1=CC=CC(NN=CC2=NC3=CC=C(F)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 32, 32, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 9, 32, 43, 43, 43, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042191 none O=C([O-])C1=CC=CC(NN=CC2=NC3=CC=C(F)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 42, 43, 43, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 42, 43, 43, 31, 6, 1, 1, 1, 43] 43
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042191 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042191
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042191/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042191/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042191
Building REAL300000042192
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042192'
/scratch/stefan/7769623/working/building/REAL300000042192 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042192

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042192/0 /scratch/stefan/7769623/working/building/REAL300000042192 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/213
`/scratch/stefan/7769623/working/3D/213' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=C1)

`REAL300000042192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042192 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 46, 46, 28, 28, 100, 133, 201, 201, 46, 46, 1, 1, 1, 1, 9, 28, 46, 46, 133, 133, 201, 201, 201, 201, 201, 46, 46, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 621
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042192 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 161, 91, 91, 31, 29, 51, 51, 29, 10, 1, 1, 1, 1, 51, 51, 201, 201, 201, 201, 161, 91, 51, 51, 10, 10, 1, 1, 1, 1, 1, 51, 51, 201] 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, 39])
total number of confs: 592
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042192 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCC3CC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 20, 3, 3, 1, 1, 1, 1, 1, 1, 6, 17, 51, 51, 1, 1, 46, 46, 46, 46, 20, 3, 1, 1, 17, 17, 51, 51, 51, 51, 51, 1, 1, 46] 201
rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 39])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042192 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042192
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042192/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042192
Building REAL300000042193
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042193'
/scratch/stefan/7769623/working/building/REAL300000042193 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042193

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042193/0 /scratch/stefan/7769623/working/building/REAL300000042193 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/214
`/scratch/stefan/7769623/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)CCC2=C1OC)

`REAL300000042193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042193 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)CCC2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 40, 40, 41, 41, 40, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 9, 40, 40, 40, 40, 1, 1, 1, 1, 4, 4, 4] 65
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 18, 19, 20, 21, 22, 36, 27, 28, 37, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 76
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042193 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)CCC2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 40, 40, 40, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 40, 40, 40, 64, 65, 65, 65, 40, 40, 10, 1, 1, 1, 1, 40, 40, 40, 40, 64, 64, 64] 65
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 160
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042193 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042193
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042193/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042193
Building REAL300000042194
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042194'
/scratch/stefan/7769623/working/building/REAL300000042194 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042194

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042194/0 /scratch/stefan/7769623/working/building/REAL300000042194 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/215
`/scratch/stefan/7769623/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C(F)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Cl)

`REAL300000042194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042194 none N#CC1=C(F)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 10, 30, 49, 49, 49, 49] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042194 none N#CC1=C(F)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 41, 41, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 41, 13, 1, 1, 1, 1] 49
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25])
total number of confs: 84
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042194 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042194
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042194/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042194
Building REAL300000042195
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042195'
/scratch/stefan/7769623/working/building/REAL300000042195 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042195

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042195/0 /scratch/stefan/7769623/working/building/REAL300000042195 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/216
`/scratch/stefan/7769623/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C=C(C(C)N=NC3=CC=CC(C(=O)[O-])=C3)OC2=C1)

`REAL300000042195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042195 none CC1=CC=C2C=C(C(C)N=NC3=CC=CC(C(=O)[O-])=C3)OC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 83, 83, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 123, 123, 123, 123, 1] 123
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 26, 27, 28, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042195 none CC1=CC=C2C=C(C(C)N=NC3=CC=CC(C(=O)[O-])=C3)OC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 123, 123, 123, 37, 8, 37, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 123, 123, 123, 123, 123, 123, 123, 123, 123, 37, 37, 37, 37, 1, 1, 1, 1, 123] 123
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37])
total number of confs: 237
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042195 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042195/1 /scratch/stefan/7769623/working/building/REAL300000042195 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/217
`/scratch/stefan/7769623/working/3D/217' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=C(C)C=C2O1)

`REAL300000042195.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042195/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042195 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34, 27, 27, 27, 8, 1, 1, 1, 1, 35, 35, 34, 35, 35, 35, 35] 35
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 78
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042195 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=C(C)C=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 6, 22, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 35, 35, 35, 34, 1, 1, 1, 2, 2, 2, 1] 35
rigid atoms, others: [32, 1, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36])
total number of confs: 89
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042195 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042195
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042195/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042195/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042195
Building REAL300000042196
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042196'
/scratch/stefan/7769623/working/building/REAL300000042196 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042196

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042196/0 /scratch/stefan/7769623/working/building/REAL300000042196 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/218
`/scratch/stefan/7769623/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=C(Cl)S2)=C1)

`REAL300000042196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042196 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 16, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 41, 41, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 13, 41, 63, 1] 63
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042196 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=C(Cl)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 16, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 49, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 49, 9, 1, 63] 63
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 25])
total number of confs: 137
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042196 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042196
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042196/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042196
Building REAL300000042197
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042197'
/scratch/stefan/7769623/working/building/REAL300000042197 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042197

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042197/0 /scratch/stefan/7769623/working/building/REAL300000042197 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/219
`/scratch/stefan/7769623/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C(Cl)=C2Cl)=C1)

`REAL300000042197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042197 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 11, 35, 39, 39, 1] 39
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042197 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 28, 8, 1, 1, 39] 39
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042197 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042197
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042197/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042197
Building REAL300000042198
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042198'
/scratch/stefan/7769623/working/building/REAL300000042198 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042198

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042198/0 /scratch/stefan/7769623/working/building/REAL300000042198 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/220
`/scratch/stefan/7769623/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CSC(Cl)=C2Cl)=C1)

`REAL300000042198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042198 none O=C([O-])C1=CC=CC(NN=CC2=CSC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 11, 35, 43, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042198 none O=C([O-])C1=CC=CC(NN=CC2=CSC(Cl)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 34, 9, 1, 43] 43
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 25])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042198 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042198
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042198/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042198
Building REAL300000042199
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042199'
/scratch/stefan/7769623/working/building/REAL300000042199 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042199

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042199/0 /scratch/stefan/7769623/working/building/REAL300000042199 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/221
`/scratch/stefan/7769623/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C2=CC=CC=C2)CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1)

`REAL300000042199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042199 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 1, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 29, 29, 29, 29, 1, 1] 44
rigid atoms, others: [0, 1, 2, 35, 33, 32, 8, 9, 10, 11, 34, 40, 22, 41, 31] set([3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39])
total number of confs: 55
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: REAL300000042199 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [29, 29, 29, 44, 44, 44, 44, 44, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 29, 44, 44, 44, 44, 44, 29, 29, 29, 29, 29, 1, 1, 1, 1, 29, 29] 44
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 97
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042199 none CC1(C2=CC=CC=C2)CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 44, 44, 44, 44, 6, 6] 44
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 68
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042199 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042199
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042199/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042199
Building REAL300000042200
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042200'
/scratch/stefan/7769623/working/building/REAL300000042200 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042200

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042200/0 /scratch/stefan/7769623/working/building/REAL300000042200 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/222
`/scratch/stefan/7769623/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=C1)

`REAL300000042200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042200 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 42, 42, 86, 86, 86, 77, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 13, 42, 86, 86, 86, 1] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042200 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 86, 85, 86, 86, 55, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 85, 86, 86, 55, 10, 1, 1, 1, 86] 86
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042200 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042200
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042200/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042200
Building REAL300000042201
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042201'
/scratch/stefan/7769623/working/building/REAL300000042201 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042201

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042201/0 /scratch/stefan/7769623/working/building/REAL300000042201 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/223
`/scratch/stefan/7769623/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(F)(F)F)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042201 none CC1=CC(C(F)(F)F)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 2, 2, 2, 1, 1, 1, 1, 10, 10, 47, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 1, 10, 47, 59, 59, 59, 59] 59
rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 26, 27, 28] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042201 none CC1=CC(C(F)(F)F)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 43, 43, 59, 59, 59, 59, 59, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 59, 59, 59, 59, 59, 59, 43, 12, 1, 1, 1, 1] 59
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 215
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042201 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042201
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042201/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042201
Building REAL300000042202
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042202'
/scratch/stefan/7769623/working/building/REAL300000042202 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042202

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042202/0 /scratch/stefan/7769623/working/building/REAL300000042202 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/224
`/scratch/stefan/7769623/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C3OCC(=O)NC3=C2)=CC=C1)

`REAL300000042202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042202 none O=C([O-])C1=CC(NN=CC2=CC=C3OCC(=O)NC3=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 42, 42, 71, 71, 71, 71, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 12, 42, 72, 72, 72, 72, 72, 72, 1, 1, 1] 72
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042202 none O=C([O-])C1=CC(NN=CC2=CC=C3OCC(=O)NC3=C2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 47, 9, 1, 1, 1, 1, 1, 1, 72, 72, 72] 72
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 20, 21, 22, 23, 24, 25, 33])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042202 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042202
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042202/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042202
Building REAL300000042203
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042203'
/scratch/stefan/7769623/working/building/REAL300000042203 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042203

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042203/0 /scratch/stefan/7769623/working/building/REAL300000042203 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/225
`/scratch/stefan/7769623/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2N=C(CN=NC3=CC=CC(C(=O)[O-])=C3)SC2=C1)

`REAL300000042203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042203 none COC1=CC=C2N=C(CN=NC3=CC=CC(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 201, 201, 201, 201, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042203 none COC1=CC=C2N=C(CN=NC3=CC=CC(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 201, 201, 201, 201, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 369
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042203 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042203/1 /scratch/stefan/7769623/working/building/REAL300000042203 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/226
`/scratch/stefan/7769623/working/3D/226' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2N=C(C=NNC3=CC=CC(C(=O)[O-])=C3)SC2=C1)

`REAL300000042203.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042203/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042203 none COC1=CC=C2N=C(C=NNC3=CC=CC(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 40, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 3, 3, 3, 1, 1, 8, 40, 88, 88, 88, 88, 1] 88
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042203 none COC1=CC=C2N=C(C=NNC3=CC=CC(C(=O)[O-])=C3)SC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 87, 87, 88, 88, 88, 88, 51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 88, 88, 88, 88, 88, 88, 88, 88, 51, 12, 1, 1, 1, 1, 88] 88
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042203 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042203
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042203/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042203/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042203
Building REAL300000042204
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042204'
/scratch/stefan/7769623/working/building/REAL300000042204 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042204

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042204/0 /scratch/stefan/7769623/working/building/REAL300000042204 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/227
`/scratch/stefan/7769623/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C=C1)

`REAL300000042204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042204 none CC1=NC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 8, 8, 45, 68, 68, 68, 68, 68, 69, 69, 68, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8, 45, 68, 68, 68, 68, 1, 1, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 22, 36, 26, 27, 35] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042204 none CC1=NC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [68, 68, 68, 68, 68, 68, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 68, 68, 68, 69, 69, 69, 68, 68, 40, 12, 1, 1, 1, 1, 68, 68, 68] 69
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042204 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042204
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042204/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042204
Building REAL300000042205
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042205'
/scratch/stefan/7769623/working/building/REAL300000042205 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042205

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042205/0 /scratch/stefan/7769623/working/building/REAL300000042205 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/228
`/scratch/stefan/7769623/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2F)=C1)

`REAL300000042205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042205 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 32, 32, 144, 167, 167, 167, 167, 167, 32, 72, 72, 50, 72, 72, 72, 72, 1, 1, 1, 1, 8, 144, 144, 167, 167, 167, 167, 72, 72, 72, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 666
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042205 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 30, 7, 7, 1, 7, 37, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 30, 37, 37, 55, 55, 55, 55, 1, 1, 1, 72] 201
rigid atoms, others: [37, 38, 39, 10, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40])
total number of confs: 270
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042205 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=N2)C2=CC=C(Cl)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 167, 167, 167, 167, 167, 167, 88, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 28, 55, 55, 37, 55, 55, 55, 55, 167, 167, 167, 167, 88, 7, 7, 1, 1, 1, 1, 55, 55, 55, 167] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 471
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042205 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042205
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042205/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042205
Building REAL300000042206
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042206'
/scratch/stefan/7769623/working/building/REAL300000042206 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042206

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042206/0 /scratch/stefan/7769623/working/building/REAL300000042206 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/229
`/scratch/stefan/7769623/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCCCC1)

`REAL300000042206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042206 none COCCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 5, 1, 1, 1, 10, 60, 60, 148, 148, 148, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 17, 17, 17, 7, 7, 5, 5, 10, 10, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [19, 3, 4, 5, 38, 39, 40, 41, 42, 43, 44, 17, 18, 35, 20, 21, 36, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 266
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042206 none COCCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 178, 135, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 142, 148, 148, 148, 141, 201, 201, 201, 190, 190, 184, 184, 40, 40, 1, 1, 1, 1, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148] 201
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 802
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042206 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042206
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042206/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042206
Building REAL300000042207
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042207'
/scratch/stefan/7769623/working/building/REAL300000042207 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042207

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042207/0 /scratch/stefan/7769623/working/building/REAL300000042207 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/230
`/scratch/stefan/7769623/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl)

`REAL300000042207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042207 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [83, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 109, 109, 48, 90, 109, 109, 109, 83, 83, 83, 83, 83, 10, 1, 1, 1, 1, 109, 109, 109] 115
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 563
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042207 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [25, 9, 1, 9, 9, 51, 109, 109, 109, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 51, 109, 109, 109, 109, 1, 1, 1] 115
rigid atoms, others: [32, 33, 2, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 279
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042207 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042207
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042207/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042207
Building REAL300000042208
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042208'
/scratch/stefan/7769623/working/building/REAL300000042208 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042208

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042208/0 /scratch/stefan/7769623/working/building/REAL300000042208 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/231
`/scratch/stefan/7769623/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1)

`REAL300000042208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042208 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 114, 114, 114, 114, 115, 115, 114, 114, 52, 52, 52, 12, 1, 1, 1, 1, 114, 114, 114, 115, 115, 115, 115, 115, 115, 115, 114] 115
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 183
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042208 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N(C(C)C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 49, 114, 114, 114, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 5, 5, 1, 1, 10, 10, 10, 48, 114, 114, 114, 114, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1] 115
rigid atoms, others: [1, 40, 13, 14, 15, 16, 17, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 238
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042208 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042208
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042208/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042208
Building REAL300000042209
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042209'
/scratch/stefan/7769623/working/building/REAL300000042209 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042209

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042209/0 /scratch/stefan/7769623/working/building/REAL300000042209 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/232
`/scratch/stefan/7769623/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1)

`REAL300000042209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042209 none CN1C=C(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 10, 1, 1, 2, 2, 2, 1, 10, 50, 50, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 34, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 390
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042209 none CN1C=C(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 127, 127, 127, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 127, 201, 201, 201, 201, 201, 201, 127, 30, 30, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 356
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042209 none CN1C=C(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 1, 1, 9, 61, 61, 127, 127, 127, 127, 127, 127, 127, 127, 1, 10, 10, 11, 11, 11, 10, 1, 9, 9, 127, 127, 127, 127, 10] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042209 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042209/1 /scratch/stefan/7769623/working/building/REAL300000042209 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/233
`/scratch/stefan/7769623/working/3D/233' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1)

`REAL300000042209.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042209/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042209 none CN1C=C(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 111, 123, 123, 123, 123, 123, 123, 123, 123, 12, 1, 1, 2, 2, 2, 1, 12, 50, 111, 123, 123, 123, 123, 1] 123
rigid atoms, others: [0, 1, 2, 3, 4, 34, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042209 none CN1C=C(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 74, 74, 74, 74, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 74, 123, 123, 123, 123, 123, 123, 74, 32, 6, 1, 1, 1, 1, 123] 123
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 198
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042209 none CN1C=C(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 39, 74, 74, 74, 74, 74, 74, 74, 74, 1, 12, 12, 13, 13, 13, 12, 1, 7, 39, 74, 74, 74, 74, 12] 123
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042209 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042209
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042209/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042209/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042209
Building REAL300000042210
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042210'
/scratch/stefan/7769623/working/building/REAL300000042210 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042210

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042210/0 /scratch/stefan/7769623/working/building/REAL300000042210 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/234
`/scratch/stefan/7769623/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=C1)

`REAL300000042210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042210 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 75, 75, 75, 186, 201, 201, 187, 201, 201, 201, 75, 75, 1, 1, 1, 1, 9, 31, 75, 187, 187, 201, 201, 201, 201, 75, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 665
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042210 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 170, 62, 62, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 170, 62, 19, 4, 4, 1, 1, 1, 1, 19, 201] 201
rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042210 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 39, 6, 6, 1, 1, 1, 1, 1, 9, 19, 19, 9, 19, 19, 19, 1, 1, 75, 75, 75, 75, 38, 6, 1, 9, 9, 19, 19, 19, 19, 1, 75] 201
rigid atoms, others: [37, 10, 11, 12, 13, 14, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042210 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042210
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042210/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042210
Building REAL300000042211
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042211'
/scratch/stefan/7769623/working/building/REAL300000042211 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042211

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042211/0 /scratch/stefan/7769623/working/building/REAL300000042211 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/235
`/scratch/stefan/7769623/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)SC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042211 none CC(C)SC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 10, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 93, 93, 93, 93, 93, 93, 93, 93, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 9, 50, 93, 93, 93, 93] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042211 none CC(C)SC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 93, 93, 93, 77, 93, 93, 93, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 30, 6, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 382
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042211 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042211
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042211/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042211
Building REAL300000042212
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042212'
/scratch/stefan/7769623/working/building/REAL300000042212 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042212

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042212/0 /scratch/stefan/7769623/working/building/REAL300000042212 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/236
`/scratch/stefan/7769623/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N(C(C)(C)C)N=C1)

`REAL300000042212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042212 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N(C(C)(C)C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 72, 72, 72, 72, 72, 72, 72, 72, 72, 38, 38, 38, 10, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 124
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042212 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N(C(C)(C)C)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 44, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 44, 72, 72, 72, 72, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 72
rigid atoms, others: [1, 43, 13, 14, 15, 16, 17, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 172
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042212 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042212
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042212/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042212
Building REAL300000042213
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042213'
/scratch/stefan/7769623/working/building/REAL300000042213 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042213

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042213/0 /scratch/stefan/7769623/working/building/REAL300000042213 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/237
`/scratch/stefan/7769623/working/3D/237' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042213 none N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 85, 85, 167, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 6, 19, 19, 19, 85, 167, 201, 201, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 501
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042213 none N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 83, 83, 83, 83, 83, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 144, 144, 83, 83, 83, 30, 6, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 525
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042213 none N#CC1=CC=CC=C1CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 44, 83, 83, 83, 83, 83, 84, 84, 83, 19, 19, 19, 19, 8, 8, 1, 1, 1, 10, 44, 83, 83, 83, 83] 201
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042213 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042213
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042213/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042213
Building REAL300000042214
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042214'
/scratch/stefan/7769623/working/building/REAL300000042214 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042214

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042214/0 /scratch/stefan/7769623/working/building/REAL300000042214 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/238
`/scratch/stefan/7769623/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=CC=C2S1)

`REAL300000042214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042214 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 63, 63, 63, 63, 62, 63, 63, 63, 41, 41, 41, 10, 1, 1, 1, 1, 63, 63, 63, 63, 63] 63
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34])
total number of confs: 111
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042214 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=CC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 38, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 38, 63, 63, 63, 63, 1, 1, 1, 1, 1] 63
rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 135
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042214 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042214
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042214/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042214
Building REAL300000042215
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042215'
/scratch/stefan/7769623/working/building/REAL300000042215 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042215

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042215/0 /scratch/stefan/7769623/working/building/REAL300000042215 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/239
`/scratch/stefan/7769623/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Br)C(Cl)=C32)=CC=C1)

`REAL300000042215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042215 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Br)C(Cl)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 10, 18, 18, 18, 1, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042215 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Br)C(Cl)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 18, 19, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 7, 1, 1, 1, 18, 18, 18] 19
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042215 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042215
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042215/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042215
Building REAL300000042216
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042216'
/scratch/stefan/7769623/working/building/REAL300000042216 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042216

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042216/0 /scratch/stefan/7769623/working/building/REAL300000042216 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/240
`/scratch/stefan/7769623/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCS(=O)(=O)C1=C(Cl)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042216 none CCS(=O)(=O)C1=C(Cl)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 34, 83, 83, 83, 83, 83, 83, 83, 83, 19, 19, 19, 19, 19, 1, 1, 1, 7, 34, 83, 83, 83, 83] 104
rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042216 none CCS(=O)(=O)C1=C(Cl)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 102, 83, 102, 102, 83, 83, 83, 50, 83, 83, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 104, 104, 104, 104, 104, 83, 83, 83, 29, 8, 1, 1, 1, 1] 104
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 391
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042216 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042216
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042216/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042216
Building REAL300000042217
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042217'
/scratch/stefan/7769623/working/building/REAL300000042217 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042217

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042217/0 /scratch/stefan/7769623/working/building/REAL300000042217 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/241
`/scratch/stefan/7769623/working/3D/241' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(Br)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042217 none COC1=C(Br)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 1, 1, 1, 5, 18, 32, 32, 32, 32] 34
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26] set([0, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042217 none COC1=C(Br)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 32, 32, 32, 32, 32, 32, 32, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 32, 32, 32, 26, 8, 1, 1, 1, 1] 34
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042217 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042217
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042217/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042217
Building REAL300000042218
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042218'
/scratch/stefan/7769623/working/building/REAL300000042218 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042218

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042218/0 /scratch/stefan/7769623/working/building/REAL300000042218 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/242
`/scratch/stefan/7769623/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl)

`REAL300000042218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042218 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 67, 67, 24, 42, 183, 201, 201, 185, 183, 201, 201, 67, 67, 67, 25, 25, 25, 4, 1, 1, 1, 1, 67, 67, 201, 201, 201, 200, 67] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 474
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042218 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 19, 69, 69, 161, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 69, 69, 69, 161, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19] 201
rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 502
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042218 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 33, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 9, 19, 19, 11, 9, 19, 19, 1, 1, 1, 7, 7, 7, 33, 67, 67, 67, 67, 1, 1, 19, 19, 19, 19, 1] 201
rigid atoms, others: [1, 36, 37, 42, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 175
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042218 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042218
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042218/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042218
Building REAL300000042219
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042219'
/scratch/stefan/7769623/working/building/REAL300000042219 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042219

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042219/0 /scratch/stefan/7769623/working/building/REAL300000042219 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/243
`/scratch/stefan/7769623/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CCC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21)

`REAL300000042219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042219 none CN1C(=O)CCC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 49, 75, 75, 75, 75, 1, 1] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 38, 21, 22, 23, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26])
total number of confs: 159
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042219 none CN1C(=O)CCC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [75, 74, 75, 75, 75, 75, 75, 75, 41, 41, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 75, 72, 75, 75, 75, 75, 75, 75, 75, 75, 41, 12, 1, 1, 1, 1, 75, 75] 75
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 142
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042219 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042219
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042219/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042219
Building REAL300000042220
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042220'
/scratch/stefan/7769623/working/building/REAL300000042220 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042220

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042220/0 /scratch/stefan/7769623/working/building/REAL300000042220 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/244
`/scratch/stefan/7769623/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042220 none COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 12, 12, 52, 153, 153, 153, 153, 153, 153, 153, 153, 4, 4, 4, 1, 1, 3, 3, 3, 3, 1, 12, 52, 153, 153, 153, 153] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 12, 13, 14, 35, 29, 30] set([0, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042220 none COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 153, 153, 153, 153, 153, 153, 201, 201, 201, 201, 201, 153, 71, 71, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 153, 153, 201, 201, 201, 201, 153, 71, 12, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 416
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042220 none COC1=CC=C(C2=CC=NC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 24, 24, 89, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 7, 3, 3, 1, 1, 1, 1, 3, 24, 89, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 379
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042220 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042220
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042220/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042220
Building REAL300000042221
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042221'
/scratch/stefan/7769623/working/building/REAL300000042221 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042221

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042221/0 /scratch/stefan/7769623/working/building/REAL300000042221 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/245
`/scratch/stefan/7769623/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C(Cl)=C1)

`REAL300000042221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042221 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 92, 92, 90, 92, 92, 92, 92, 52, 52, 52, 10, 1, 1, 1, 1, 92, 92, 184, 92] 184
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 340
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042221 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 53, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 53, 92, 92, 92, 92, 1, 1, 2, 1] 184
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 195
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042221 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042221/1 /scratch/stefan/7769623/working/building/REAL300000042221 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/246
`/scratch/stefan/7769623/working/3D/246' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C(Cl)=C1)

`REAL300000042221.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042221/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042221 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 45, 45, 43, 45, 45, 45, 45, 24, 24, 24, 5, 1, 1, 1, 1, 45, 45, 45] 45
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 86
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042221 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [9, 1, 9, 9, 37, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 45, 45, 45, 45, 1, 1, 1] 45
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 105
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042221 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042221
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042221/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042221/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042221
Building REAL300000042222
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042222'
/scratch/stefan/7769623/working/building/REAL300000042222 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042222

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042222/0 /scratch/stefan/7769623/working/building/REAL300000042222 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/247
`/scratch/stefan/7769623/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)C)=N1)

`REAL300000042222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042222 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 86, 86, 86, 86, 107, 107, 86, 45, 45, 45, 10, 1, 1, 1, 1, 86, 107, 107, 107, 107, 107, 107, 107] 107
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 267
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042222 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 33, 86, 86, 86, 86, 86, 87, 87, 86, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 33, 86, 86, 86, 86, 1, 10, 11, 11, 11, 11, 11, 11] 107
rigid atoms, others: [1, 13, 14, 15, 16, 17, 20, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 203
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042222 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042222/1 /scratch/stefan/7769623/working/building/REAL300000042222 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/248
`/scratch/stefan/7769623/working/3D/248' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=CS1)

`REAL300000042222.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042222/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042222 none CC(C)C1=NC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 1, 1, 1, 1, 12, 12, 75, 75, 170, 170, 170, 170, 170, 170, 170, 170, 1, 1, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 170, 170, 170, 170, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 36] set([0, 2, 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, 35])
total number of confs: 301
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042222 none CC(C)C1=NC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 170, 201, 170, 170, 48, 8, 48, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 170, 170, 201, 201, 201, 201, 201, 201, 201, 48, 48, 48, 48, 1, 1, 1, 1, 170] 201
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 494
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042222 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042222
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042222/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042222/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042222
Building REAL300000042223
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042223'
/scratch/stefan/7769623/working/building/REAL300000042223 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042223

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042223/0 /scratch/stefan/7769623/working/building/REAL300000042223 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/249
`/scratch/stefan/7769623/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1)

`REAL300000042223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042223 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 6, 15, 17, 17, 34, 17, 1] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042223 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [17, 17, 17, 17, 16, 17, 17, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 16, 17, 17, 13, 6, 1, 1, 2, 1, 17] 34
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 29, 31])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042223 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042223
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042223/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042223
Building REAL300000042224
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042224'
/scratch/stefan/7769623/working/building/REAL300000042224 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042224

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042224/0 /scratch/stefan/7769623/working/building/REAL300000042224 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/250
`/scratch/stefan/7769623/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(C)(C)O)C=C1)

`REAL300000042224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042224 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(C)(C)O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 88, 88, 40, 40, 117, 117, 117, 88, 88, 40, 40, 40, 8, 1, 1, 1, 1, 88, 88, 117, 117, 117, 117, 117, 117, 351, 88, 88] 357
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 925
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042224 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(C)(C)O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 35, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 6, 6, 6, 35, 88, 88, 88, 88, 1, 1, 13, 13, 13, 13, 13, 13, 36, 1, 1] 357
rigid atoms, others: [32, 1, 40, 41, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 244
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042224 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042224
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042224/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042224
Building REAL300000042225
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042225'
/scratch/stefan/7769623/working/building/REAL300000042225 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042225

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042225/0 /scratch/stefan/7769623/working/building/REAL300000042225 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/251
`/scratch/stefan/7769623/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(C)=C1O)

`REAL300000042225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042225 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(C)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 71, 71, 71, 65, 71, 71, 71, 71, 41, 41, 41, 10, 1, 1, 1, 1, 71, 71, 71, 71, 71, 142] 142
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 292
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042225 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CC(C)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 43, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 43, 71, 71, 71, 71, 1, 1, 2, 2, 2, 2] 142
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 165
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042225 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042225
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042225/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042225
Building REAL300000042226
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042226'
/scratch/stefan/7769623/working/building/REAL300000042226 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042226

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042226/0 /scratch/stefan/7769623/working/building/REAL300000042226 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/252
`/scratch/stefan/7769623/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F)

`REAL300000042226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042226 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 87, 87, 87, 87, 87, 87, 87, 43, 43, 43, 43, 1, 1, 1, 1, 87, 87] 87
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 208
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042226 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [10, 1, 10, 55, 55, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 87, 87, 87, 87, 1, 1] 87
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042226 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042226/1 /scratch/stefan/7769623/working/building/REAL300000042226 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/253
`/scratch/stefan/7769623/working/3D/253' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F)

`REAL300000042226.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042226/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042226 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 59, 59, 59, 59, 59, 59, 59, 31, 31, 31, 8, 1, 1, 1, 1, 59, 59] 60
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 104
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042226 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [11, 1, 11, 11, 47, 59, 59, 59, 59, 59, 60, 60, 59, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 47, 59, 59, 59, 59, 1, 1] 60
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 145
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042226 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042226
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042226/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042226/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042226
Building REAL300000042227
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042227'
/scratch/stefan/7769623/working/building/REAL300000042227 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042227

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042227/0 /scratch/stefan/7769623/working/building/REAL300000042227 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/254
`/scratch/stefan/7769623/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCS(=O)(=O)CC1)

`REAL300000042227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042227 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCS(=O)(=O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 72, 72, 72, 72, 72, 72, 72, 47, 47, 47, 47, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 240
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042227 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCS(=O)(=O)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 46, 46, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 72
rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 123
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042227 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042227
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042227/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042227
Building REAL300000042228
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042228'
/scratch/stefan/7769623/working/building/REAL300000042228 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042228

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042228/0 /scratch/stefan/7769623/working/building/REAL300000042228 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/255
`/scratch/stefan/7769623/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042228 none C#CCOC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 113, 113, 113, 113, 113, 113, 113, 113, 45, 45, 45, 1, 1, 1, 10, 55, 113, 113, 113, 113] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 353
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042228 none C#CCOC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 168, 113, 113, 113, 76, 113, 113, 113, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 113, 113, 113, 48, 10, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 565
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042228 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042228
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042228/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042228
Building REAL300000042229
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042229'
/scratch/stefan/7769623/working/building/REAL300000042229 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042229

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042229/0 /scratch/stefan/7769623/working/building/REAL300000042229 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/256
`/scratch/stefan/7769623/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCCCC2=CC=C3OCCC3=C2)=C1)

`REAL300000042229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042229 none O=C([O-])C1=CC=CC(N=NCCCC2=CC=C3OCCC3=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 45, 55, 113, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 44, 45, 77, 77, 105, 105, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 696
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042229 none O=C([O-])C1=CC=CC(N=NCCCC2=CC=C3OCCC3=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 138, 138, 27, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 27, 27, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39])
total number of confs: 367
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042229 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042229
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042229/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042229
Building REAL300000042230
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042230'
/scratch/stefan/7769623/working/building/REAL300000042230 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042230

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042230/0 /scratch/stefan/7769623/working/building/REAL300000042230 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/257
`/scratch/stefan/7769623/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1)

`REAL300000042230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042230 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 23, 23, 23, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 149
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: REAL300000042230 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 8, 47, 47, 47, 47, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 47
rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 87
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042230 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1(C2=CC=CC=C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 24, 24, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 47, 47, 47, 47, 4, 4, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 47
rigid atoms, others: [1, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 89
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042230 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042230
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042230/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042230
Building REAL300000042231
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042231'
/scratch/stefan/7769623/working/building/REAL300000042231 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042231

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042231/0 /scratch/stefan/7769623/working/building/REAL300000042231 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/258
`/scratch/stefan/7769623/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21)

`REAL300000042231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042231 none CCN1N=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 8, 8, 46, 85, 85, 85, 85, 85, 86, 86, 85, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5, 8, 46, 85, 85, 85, 85, 1, 1, 1, 1] 115
rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 21, 22, 36, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042231 none CCN1N=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [114, 85, 85, 85, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 85, 85, 85, 85, 85, 115, 115, 115, 114, 114, 50, 10, 1, 1, 1, 1, 85, 85, 85, 85] 115
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 314
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042231 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042231/1 /scratch/stefan/7769623/working/building/REAL300000042231 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/259
`/scratch/stefan/7769623/working/3D/259' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=C(CN=NC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21)

`REAL300000042231.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042231/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042231 none CCN1N=C(CN=NC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 9, 62, 62, 137, 137, 137, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 5, 8, 8, 137, 137, 137, 137, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 21, 22, 36, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 222
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042231 none CCN1N=C(CN=NC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 136, 136, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 136, 137, 137, 137, 137, 136, 201, 201, 201, 201, 201, 47, 47, 1, 1, 1, 1, 137, 137, 137, 136] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 663
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042231 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042231
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042231/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042231/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042231
Building REAL300000042232
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042232'
/scratch/stefan/7769623/working/building/REAL300000042232 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042232

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042232/0 /scratch/stefan/7769623/working/building/REAL300000042232 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/260
`/scratch/stefan/7769623/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042232 none CCSC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [27, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 57, 112, 112, 112, 112, 112, 112, 112, 112, 1, 28, 28, 28, 27, 27, 1, 1, 1, 11, 57, 112, 112, 112, 112, 1] 182
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 35, 20, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 306
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042232 none CCSC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 181, 112, 112, 111, 112, 112, 57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 112, 182, 182, 182, 182, 182, 111, 112, 112, 57, 12, 1, 1, 1, 1, 112] 182
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 283
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042232 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042232
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042232/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042232
Building REAL300000042233
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042233'
/scratch/stefan/7769623/working/building/REAL300000042233 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042233

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042233/0 /scratch/stefan/7769623/working/building/REAL300000042233 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/261
`/scratch/stefan/7769623/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F)

`REAL300000042233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042233 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 35, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 2, 2, 2, 1, 6, 34, 53, 53, 53, 53, 2, 2, 2, 7, 7, 6, 7] 136
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 144
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042233 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 35, 35, 100, 136, 136, 136, 136, 136, 136, 136, 136, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 35, 100, 136, 136, 136, 136, 7, 7, 7, 1, 1, 1, 1] 136
rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 318
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042233 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=CC=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [53, 52, 53, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 53, 52, 52, 136, 136, 89, 136, 136, 136, 53, 53, 53, 53, 28, 6, 1, 1, 1, 1, 53, 53, 53, 136, 136, 136, 136] 136
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 445
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042233 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042233
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042233/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042233
Building REAL300000042234
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042234'
/scratch/stefan/7769623/working/building/REAL300000042234 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042234

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042234/0 /scratch/stefan/7769623/working/building/REAL300000042234 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/262
`/scratch/stefan/7769623/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(C(F)(F)F)C=C3)N=C2)=C1)

`REAL300000042234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042234 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(C(F)(F)F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 71, 71, 71, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71, 1, 1, 1, 1, 9, 31, 71, 185, 185, 201, 201, 201, 201, 71, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 609
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042234 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(C(F)(F)F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 170, 61, 61, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 201, 201, 201, 201, 170, 61, 19, 5, 5, 1, 1, 1, 1, 19, 201] 201
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 504
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042234 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3=CC=C(C(F)(F)F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 34, 6, 6, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 71, 71, 71, 71, 33, 6, 1, 9, 9, 19, 19, 19, 19, 1, 71] 201
rigid atoms, others: [33, 40, 10, 11, 12, 13, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 41])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042234 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042234
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042234/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042234
Building REAL300000042235
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042235'
/scratch/stefan/7769623/working/building/REAL300000042235 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042235

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042235/0 /scratch/stefan/7769623/working/building/REAL300000042235 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/263
`/scratch/stefan/7769623/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(Br)C=C32)=C1)

`REAL300000042235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042235 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 28
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042235 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24])
total number of confs: 26
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042235 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042235
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042235/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042235
Building REAL300000042236
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042236'
/scratch/stefan/7769623/working/building/REAL300000042236 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042236

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042236/0 /scratch/stefan/7769623/working/building/REAL300000042236 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/264
`/scratch/stefan/7769623/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1)

`REAL300000042236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042236 none CC(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [69, 67, 69, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 125, 125, 115, 125, 125, 125, 69, 69, 69, 69, 69, 69, 69, 67, 67, 10, 1, 1, 1, 1, 125, 125, 122, 125] 137
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 371
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042236 none CC(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [36, 33, 36, 12, 1, 12, 12, 57, 125, 125, 125, 125, 125, 126, 126, 125, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 33, 33, 57, 125, 125, 125, 125, 1, 1, 1, 1] 137
rigid atoms, others: [4, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 366
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042236 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042236
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042236/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042236
Building REAL300000042237
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042237'
/scratch/stefan/7769623/working/building/REAL300000042237 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042237

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042237/0 /scratch/stefan/7769623/working/building/REAL300000042237 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/265
`/scratch/stefan/7769623/working/3D/265' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC(Br)=CC=C32)=C1)

`REAL300000042237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042237 none O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC(Br)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 38
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042237 none O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC(Br)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 19, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 19, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20] 20
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 38])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042237 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042237
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042237/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042237
Building REAL300000042238
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042238'
/scratch/stefan/7769623/working/building/REAL300000042238 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042238

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042238/0 /scratch/stefan/7769623/working/building/REAL300000042238 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/266
`/scratch/stefan/7769623/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042238 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 12, 36, 45, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 4, 4, 4, 4, 2, 2, 2, 12, 35, 45, 45, 45, 44] 45
rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042238 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 44, 44, 44, 44, 45, 45, 45, 45, 45, 44, 45, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 22, 6, 1, 1, 1, 1] 45
rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 78
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042238 none CC1=NN(C2=CC=CC=N2)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 19, 19, 36, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 19, 36, 45, 45, 45, 45] 45
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042238 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042238
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042238/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042238
Building REAL300000042239
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042239'
/scratch/stefan/7769623/working/building/REAL300000042239 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042239

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042239/0 /scratch/stefan/7769623/working/building/REAL300000042239 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/267
`/scratch/stefan/7769623/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1)

`REAL300000042239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042239 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 10, 10, 33, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 1, 10, 33, 65, 65, 65, 65, 7, 7, 7, 7, 7, 1] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 17, 18, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042239 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 25, 25, 65, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 25, 65, 80, 80, 80, 80, 1, 1, 2, 2, 2, 7] 80
rigid atoms, others: [36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 190
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042239 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NN2C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [65, 65, 65, 65, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 65, 65, 80, 80, 80, 80, 80, 65, 65, 65, 65, 65, 65, 31, 9, 1, 1, 1, 1, 80, 80, 80, 80, 80, 65] 80
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042239 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042239
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042239/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042239
Building REAL300000042240
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042240'
/scratch/stefan/7769623/working/building/REAL300000042240 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042240

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042240/0 /scratch/stefan/7769623/working/building/REAL300000042240 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/268
`/scratch/stefan/7769623/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=C1)

`REAL300000042240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042240 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 32, 32, 32, 32, 54, 54, 54, 54, 54, 54, 54, 54, 54, 32, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 54, 54, 54, 54, 32, 32, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 112
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: REAL300000042240 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 29, 29, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 54, 54, 54, 54, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 54] 54
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 92
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042240 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(C(F)(F)F)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 6, 6, 6, 1, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 32] 54
rigid atoms, others: [32, 33, 34, 39, 40, 9, 10, 11, 12, 13, 14, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 35, 36, 37, 38, 41])
total number of confs: 76
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042240 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042240
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042240/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042240
Building REAL300000042241
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042241'
/scratch/stefan/7769623/working/building/REAL300000042241 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042241

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042241/0 /scratch/stefan/7769623/working/building/REAL300000042241 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/269
`/scratch/stefan/7769623/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N)C([N+](=O)[O-])=C1)

`REAL300000042241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042241 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N)C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 3, 3, 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: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 103, 103, 87, 101, 103, 103, 103, 103, 103, 54, 54, 54, 10, 1, 1, 1, 1, 103, 103, 103, 103, 103] 103
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 245
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042241 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N)C([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 3, 3, 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: [11, 1, 11, 11, 61, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 61, 103, 103, 103, 103, 1, 1, 2, 2, 1] 103
rigid atoms, others: [32, 1, 35, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 223
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042241 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042241
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042241/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042241
Building REAL300000042242
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042242'
/scratch/stefan/7769623/working/building/REAL300000042242 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042242

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042242/0 /scratch/stefan/7769623/working/building/REAL300000042242 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/270
`/scratch/stefan/7769623/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(F)=CC=C21)

`REAL300000042242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042242 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(F)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 46, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 45, 71, 71, 71, 70, 1, 1, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042242 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(F)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 71, 71, 71, 71, 70, 70, 71, 71, 71, 70, 40, 12, 1, 1, 1, 1, 71, 71, 70] 71
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042242 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042242
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042242/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042242
Building REAL300000042243
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042243'
/scratch/stefan/7769623/working/building/REAL300000042243 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042243

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042243/0 /scratch/stefan/7769623/working/building/REAL300000042243 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/271
`/scratch/stefan/7769623/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3Br)C=C2)=C1)

`REAL300000042243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042243 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3Br)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 47, 47, 53, 53, 47, 53, 89, 89, 54, 89, 89, 89, 53, 53, 1, 1, 1, 1, 13, 47, 53, 53, 89, 89, 89, 89, 53, 53, 1] 89
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042243 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3Br)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 61, 15, 15, 2, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 89, 89, 89, 89, 61, 13, 7, 7, 1, 1, 1, 1, 7, 7, 89] 89
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 212
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042243 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3Br)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 53, 53, 53, 53, 53, 53, 25, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 53, 53, 53, 53, 24, 3, 1, 1, 7, 7, 2, 7, 1, 1, 53] 89
rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042243 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042243
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042243/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042243
Building REAL300000042244
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042244'
/scratch/stefan/7769623/working/building/REAL300000042244 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042244

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042244/0 /scratch/stefan/7769623/working/building/REAL300000042244 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/272
`/scratch/stefan/7769623/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1)

`REAL300000042244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042244 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 37, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 1, 9, 37, 73, 73, 73, 73, 9, 9, 9, 9, 9, 1] 97
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 17, 18, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042244 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [9, 9, 8, 9, 9, 9, 33, 33, 76, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 33, 76, 97, 97, 97, 97, 1, 2, 2, 2, 1, 9] 97
rigid atoms, others: [36, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41])
total number of confs: 236
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042244 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 97, 97, 97, 97, 97, 73, 73, 73, 73, 73, 73, 34, 9, 1, 1, 1, 1, 97, 97, 97, 97, 97, 73] 97
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042244 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042244
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042244/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042244
Building REAL300000042245
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042245'
/scratch/stefan/7769623/working/building/REAL300000042245 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042245

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042245/0 /scratch/stefan/7769623/working/building/REAL300000042245 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/273
`/scratch/stefan/7769623/working/3D/273' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=C1)

`REAL300000042245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042245 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 71, 71, 164, 164, 164, 164, 164, 172, 172, 164, 172, 172, 172, 1, 1, 1, 1, 13, 71, 164, 164, 172, 172, 172, 172, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 289
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042245 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [172, 172, 172, 172, 172, 172, 172, 110, 23, 23, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 110, 23, 5, 5, 1, 1, 1, 1, 172] 172
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 359
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042245 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [164, 164, 164, 164, 164, 164, 164, 80, 13, 13, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 5, 5, 164, 164, 164, 164, 80, 13, 1, 1, 5, 5, 5, 5, 164] 172
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 326
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042245 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042245
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042245/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042245
Building REAL300000042246
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042246'
/scratch/stefan/7769623/working/building/REAL300000042246 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042246

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042246/0 /scratch/stefan/7769623/working/building/REAL300000042246 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/274
`/scratch/stefan/7769623/working/3D/274' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042246 none CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 35, 35, 100, 113, 113, 113, 113, 113, 113, 113, 113, 2, 2, 2, 1, 1, 1, 1, 9, 9, 35, 100, 113, 113, 113, 113] 113
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30] set([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: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042246 none CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 113, 113, 88, 88, 88, 88, 88, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 113, 113, 113, 113, 113, 113, 113, 88, 88, 31, 6, 1, 1, 1, 1] 113
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 176
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042246 none CC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 51, 88, 88, 88, 88, 88, 88, 88, 88, 9, 9, 9, 9, 9, 9, 9, 1, 1, 12, 51, 88, 88, 88, 88] 113
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042246 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042246
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042246/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042246
Building REAL300000042247
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042247'
/scratch/stefan/7769623/working/building/REAL300000042247 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042247

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042247/0 /scratch/stefan/7769623/working/building/REAL300000042247 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/275
`/scratch/stefan/7769623/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=N1)

`REAL300000042247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042247 none CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 59, 59, 109, 118, 118, 118, 118, 118, 118, 118, 118, 12, 1, 1, 2, 2, 2, 1, 12, 12, 59, 109, 118, 118, 118, 118, 1] 118
rigid atoms, others: [0, 1, 2, 3, 4, 35, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042247 none CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 70, 70, 70, 70, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 117, 118, 118, 118, 118, 118, 70, 70, 34, 8, 1, 1, 1, 1, 118] 118
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 193
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042247 none CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 12, 1, 1, 1, 1, 1, 1, 8, 8, 38, 70, 70, 70, 70, 70, 70, 70, 70, 1, 12, 12, 13, 13, 13, 12, 1, 1, 8, 38, 70, 70, 70, 70, 12] 118
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042247 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042247
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042247/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042247
Building REAL300000042248
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042248'
/scratch/stefan/7769623/working/building/REAL300000042248 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042248

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042248/0 /scratch/stefan/7769623/working/building/REAL300000042248 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/276
`/scratch/stefan/7769623/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)OC)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042248 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [6, 1, 1, 1, 1, 10, 10, 10, 1, 1, 1, 6, 6, 31, 63, 63, 63, 63, 63, 64, 64, 63, 1, 6, 6, 6, 6, 6, 11, 11, 11, 1, 6, 31, 63, 63, 63, 63] 148
rigid atoms, others: [1, 2, 3, 4, 8, 9, 10, 22, 31] set([0, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042248 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', '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, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [100, 63, 63, 63, 63, 147, 147, 147, 63, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 100, 100, 100, 100, 100, 148, 148, 148, 63, 32, 8, 1, 1, 1, 1] 148
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 544
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042248 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042248
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042248/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042248
Building REAL300000042249
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042249'
/scratch/stefan/7769623/working/building/REAL300000042249 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042249

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042249/0 /scratch/stefan/7769623/working/building/REAL300000042249 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/277
`/scratch/stefan/7769623/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1)

`REAL300000042249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042249 none CC(C)(C)OC(=O)N1CCCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [20, 15, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 1, 1, 1, 1] 82
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47])
total number of confs: 114
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042249 none CC(C)(C)OC(=O)N1CCCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 82, 55, 39, 55, 39, 39, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 82, 82, 82, 82, 82, 82, 82, 82, 82, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 39, 39, 39, 39] 82
rigid atoms, others: [44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51])
total number of confs: 202
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042249 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042249
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042249/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042249
Building REAL300000042250
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042250'
/scratch/stefan/7769623/working/building/REAL300000042250 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042250

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042250/0 /scratch/stefan/7769623/working/building/REAL300000042250 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/278
`/scratch/stefan/7769623/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCN1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042250 none COCCCN1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [52, 25, 11, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 36, 36, 36, 36, 36, 36, 36, 36, 53, 53, 53, 25, 25, 11, 11, 5, 5, 1, 1, 6, 19, 36, 36, 36, 36] 94
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 243
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042250 none COCCCN1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 76, 66, 36, 36, 36, 36, 36, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 94, 94, 94, 94, 94, 76, 76, 66, 66, 36, 36, 19, 6, 1, 1, 1, 1] 94
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042250 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042250
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042250/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042250
Building REAL300000042251
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042251'
/scratch/stefan/7769623/working/building/REAL300000042251 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042251

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042251/0 /scratch/stefan/7769623/working/building/REAL300000042251 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/279
`/scratch/stefan/7769623/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(Br)=C2F)=C1)

`REAL300000042251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042251 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(Br)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 41, 41, 76, 76, 76, 75, 76, 76, 76, 76, 1, 1, 1, 1, 11, 41, 76, 76, 1] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042251 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(Br)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 55, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 55, 13, 1, 1, 76] 76
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042251 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042251
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042251/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042251
Building REAL300000042252
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042252'
/scratch/stefan/7769623/working/building/REAL300000042252 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042252

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042252/0 /scratch/stefan/7769623/working/building/REAL300000042252 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/280
`/scratch/stefan/7769623/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042252 none CC(C)(C)OC(=O)NC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 14, 17, 17, 8, 6, 8, 1, 1, 1, 1, 1, 1, 8, 8, 47, 87, 87, 87, 87, 87, 88, 88, 87, 1, 17, 17, 17, 16, 17, 16, 17, 17, 17, 6, 1, 8, 47, 87, 87, 87, 87] 201
rigid atoms, others: [35, 7, 8, 9, 10, 11, 12, 24] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042252 none CC(C)(C)OC(=O)NC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 142, 113, 142, 87, 87, 87, 87, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 87, 49, 12, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 452
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042252 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042252
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042252/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042252
Building REAL300000042253
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042253'
/scratch/stefan/7769623/working/building/REAL300000042253 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042253

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042253/0 /scratch/stefan/7769623/working/building/REAL300000042253 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/281
`/scratch/stefan/7769623/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F)

`REAL300000042253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042253 none CCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 11, 1, 1, 1, 1, 1, 1, 8, 8, 48, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 34, 34, 34, 33, 33, 1, 1, 8, 48, 108, 108, 108, 108, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 19, 20, 21, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 297
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042253 none CCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 107, 107, 108, 108, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 108, 108, 108, 201, 201, 201, 201, 201, 108, 108, 40, 8, 1, 1, 1, 1, 108] 201
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 374
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042253 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042253
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042253/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042253
Building REAL300000042254
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042254'
/scratch/stefan/7769623/working/building/REAL300000042254 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042254

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042254/0 /scratch/stefan/7769623/working/building/REAL300000042254 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/282
`/scratch/stefan/7769623/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042254 none CSC1=CC=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 97, 97, 97, 97, 97, 97, 97, 97, 7, 7, 7, 1, 1, 1, 1, 9, 9, 9, 41, 97, 97, 97, 97] 105
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 180
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042254 none CSC1=CC=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 97, 97, 97, 97, 97, 97, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 105, 105, 105, 97, 97, 97, 97, 53, 53, 53, 10, 1, 1, 1, 1] 105
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 156
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042254 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042254
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042254/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042254
Building REAL300000042255
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042255'
/scratch/stefan/7769623/working/building/REAL300000042255 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042255

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042255/0 /scratch/stefan/7769623/working/building/REAL300000042255 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/283
`/scratch/stefan/7769623/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COCC3=CC=CC(Cl)=C32)=C1)

`REAL300000042255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042255 none O=C([O-])C1=CC=CC(NN=C2COCC3=CC=CC(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 11, 25, 25, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042255 none O=C([O-])C1=CC=CC(NN=C2COCC3=CC=CC(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25] 25
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 33])
total number of confs: 42
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042255 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042255
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042255/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042255
Building REAL300000042256
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042256'
/scratch/stefan/7769623/working/building/REAL300000042256 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042256

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042256/0 /scratch/stefan/7769623/working/building/REAL300000042256 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/284
`/scratch/stefan/7769623/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=C1)

`REAL300000042256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042256 none O=C([O-])C1=CC=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 64, 64, 64, 64, 117, 117, 117, 201, 201, 201, 201, 201, 201, 64, 59, 1, 1, 1, 1, 18, 19, 64, 64, 64, 64, 64, 201, 201, 201, 201, 201, 201, 201, 64, 64, 64, 64, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 49, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 843
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042256 none O=C([O-])C1=CC=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 179, 179, 74, 22, 22, 22, 22, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 201, 74, 74, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22, 22, 22, 22, 201] 201
rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48, 49])
total number of confs: 448
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042256 none O=C([O-])C1=CC=CC(N=NCC2CCN(C(=O)OCC3=CC=CC=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 64, 64, 64, 64, 36, 36, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 22, 22, 11, 22, 22, 1, 1, 64, 64, 64, 64, 6, 6, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 22, 1, 1, 1, 1, 64] 201
rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 48, 46, 45, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 49])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042256 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042256
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042256/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042256
Building REAL300000042257
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042257'
/scratch/stefan/7769623/working/building/REAL300000042257 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042257

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042257/0 /scratch/stefan/7769623/working/building/REAL300000042257 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/285
`/scratch/stefan/7769623/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC2=CC=CC=C2C(=NNC2=CC=CC(C(=O)[O-])=C2)C1)

`REAL300000042257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042257 none CC1(C)CCC2=CC=CC=C2C(=NNC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 16, 17, 17, 16, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 1, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44] set([38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042257 none CC1(C)CCC2=CC=CC=C2C(=NNC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 8, 1, 1, 1, 1, 16, 16] 17
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 47
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042257 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042257
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042257/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042257
Building REAL300000042258
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042258'
/scratch/stefan/7769623/working/building/REAL300000042258 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042258

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042258/0 /scratch/stefan/7769623/working/building/REAL300000042258 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/286
`/scratch/stefan/7769623/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC3=CC=C(Br)C=C3S2)=C1)

`REAL300000042258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042258 none O=C([O-])C1=CC=CC(N=NCC2=NC3=CC=C(Br)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 132, 132, 132, 132, 132, 132, 132, 132, 132, 1, 1, 1, 1, 49, 48, 132, 132, 132, 1] 132
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 274
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042258 none O=C([O-])C1=CC=CC(N=NCC2=NC3=CC=C(Br)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [132, 132, 132, 132, 132, 132, 132, 57, 57, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 8, 8, 1, 1, 1, 132] 132
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042258 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042258/1 /scratch/stefan/7769623/working/building/REAL300000042258 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/287
`/scratch/stefan/7769623/working/3D/287' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC3=CC=C(Br)C=C3S2)=C1)

`REAL300000042258.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042258/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042258 none O=C([O-])C1=CC=CC(NN=CC2=NC3=CC=C(Br)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 9, 31, 44, 44, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042258 none O=C([O-])C1=CC=CC(NN=CC2=NC3=CC=C(Br)C=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 44, 44, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 43, 44, 44, 33, 8, 1, 1, 1, 44] 44
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 102
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042258 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042258
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042258/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042258/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042258
Building REAL300000042259
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042259'
/scratch/stefan/7769623/working/building/REAL300000042259 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042259

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042259/0 /scratch/stefan/7769623/working/building/REAL300000042259 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/288
`/scratch/stefan/7769623/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=C1)

`REAL300000042259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042259 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47, 71, 71, 71, 71, 109, 109, 109, 109, 71, 1, 1, 1, 1, 11, 47, 71, 109, 109, 109, 1] 109
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042259 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 92, 43, 43, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 109, 109, 109, 109, 92, 43, 13, 1, 1, 1, 109] 109
rigid atoms, others: [14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 264
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042259 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [71, 71, 71, 71, 71, 71, 71, 43, 10, 10, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 71, 71, 71, 71, 42, 10, 1, 13, 13, 13, 71] 109
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042259 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042259
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042259/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042259
Building REAL300000042260
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042260'
/scratch/stefan/7769623/working/building/REAL300000042260 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042260

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042260/0 /scratch/stefan/7769623/working/building/REAL300000042260 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/289
`/scratch/stefan/7769623/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=C(Cl)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042260 none CCOC1=C(Cl)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 32, 61, 61, 61, 61, 61, 61, 61, 61, 14, 14, 14, 14, 14, 1, 1, 1, 11, 32, 61, 61, 61, 61] 72
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 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: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042260 none CCOC1=C(Cl)C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 61, 61, 61, 61, 61, 61, 61, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 72, 72, 72, 72, 72, 61, 61, 61, 33, 7, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042260 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042260
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042260/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042260
Building REAL300000042261
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042261'
/scratch/stefan/7769623/working/building/REAL300000042261 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042261

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042261/0 /scratch/stefan/7769623/working/building/REAL300000042261 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/290
`/scratch/stefan/7769623/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1)

`REAL300000042261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042261 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 83, 83, 71, 83, 147, 147, 147, 147, 147, 83, 83, 44, 44, 44, 10, 1, 1, 1, 1, 83, 83, 147, 147, 147, 147, 147, 83, 83] 147
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 306
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: REAL300000042261 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [20, 3, 19, 20, 92, 147, 147, 147, 147, 147, 147, 147, 147, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 20, 20, 92, 147, 147, 147, 147, 7, 7, 1, 1, 1, 1, 1, 7, 7] 147
rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41])
total number of confs: 330
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042261 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 30, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 6, 6, 6, 30, 83, 83, 83, 83, 1, 1, 7, 7, 7, 7, 7, 1, 1] 147
rigid atoms, others: [1, 34, 33, 40, 41, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 156
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042261 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042261
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042261/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042261
Building REAL300000042262
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042262'
/scratch/stefan/7769623/working/building/REAL300000042262 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042262

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042262/0 /scratch/stefan/7769623/working/building/REAL300000042262 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/291
`/scratch/stefan/7769623/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(Br)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042262 none CN1N=CC(Br)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 1, 10, 36, 49, 49, 49, 49] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042262 none CN1N=CC(Br)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 40, 12, 1, 1, 1, 1] 49
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042262 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042262
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042262/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042262
Building REAL300000042263
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042263'
/scratch/stefan/7769623/working/building/REAL300000042263 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042263

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042263/0 /scratch/stefan/7769623/working/building/REAL300000042263 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/292
`/scratch/stefan/7769623/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042263 none N#CC1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042263 none N#CC1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1] 22
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 42
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042263 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042263
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042263/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042263
Building REAL300000042264
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042264'
/scratch/stefan/7769623/working/building/REAL300000042264 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042264

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042264/0 /scratch/stefan/7769623/working/building/REAL300000042264 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/293
`/scratch/stefan/7769623/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCN(C(=O)OC(C)(C)C)C1)

`REAL300000042264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042264 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 78, 78, 78, 78, 128, 128, 201, 201, 201, 201, 78, 46, 46, 46, 46, 1, 1, 1, 1, 78, 78, 78, 78, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 556
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042264 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 36, 36, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 6, 6, 15, 18, 19, 18, 1, 6, 6, 6, 6, 78, 78, 78, 78, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 48, 24, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042264 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042264
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042264/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042264
Building REAL300000042265
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042265'
/scratch/stefan/7769623/working/building/REAL300000042265 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042265

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042265/0 /scratch/stefan/7769623/working/building/REAL300000042265 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/294
`/scratch/stefan/7769623/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC=C(C(F)(F)F)S2)=C1)

`REAL300000042265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042265 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 45, 46, 123, 1] 123
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042265 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 123, 123, 123, 123, 64, 64, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 123, 123, 123, 123, 8, 8, 1, 123] 123
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042265 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042265/1 /scratch/stefan/7769623/working/building/REAL300000042265 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/295
`/scratch/stefan/7769623/working/3D/295' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC=C(C(F)(F)F)S2)=C1)

`REAL300000042265.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042265/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042265 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 11, 35, 46, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042265 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 38, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 46, 46, 46, 46, 38, 9, 1, 46] 46
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042265 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042265
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042265/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042265/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042265
Building REAL300000042266
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042266'
/scratch/stefan/7769623/working/building/REAL300000042266 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042266

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042266/0 /scratch/stefan/7769623/working/building/REAL300000042266 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/296
`/scratch/stefan/7769623/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCC(C(F)(F)F)CC1)

`REAL300000042266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042266 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCC(C(F)(F)F)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 30, 30, 30, 30, 30, 30, 30, 30, 30, 25, 25, 25, 25, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 30
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 105
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042266 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CCC(C(F)(F)F)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 3, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 30
rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 40, 39, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 64
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042266 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042266
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042266/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042266
Building REAL300000042267
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042267'
/scratch/stefan/7769623/working/building/REAL300000042267 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042267

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042267/0 /scratch/stefan/7769623/working/building/REAL300000042267 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/297
`/scratch/stefan/7769623/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=C1)

`REAL300000042267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042267 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 33, 33, 25, 33, 109, 201, 201, 201, 201, 201, 201, 33, 33, 1, 1, 1, 1, 7, 25, 33, 33, 201, 201, 201, 201, 33, 33, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 341
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042267 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 162, 75, 75, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 162, 75, 37, 37, 1, 1, 1, 1, 37, 37, 201] 201
rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042267 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=CC(F)=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 15, 3, 3, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 37, 37, 1, 1, 33, 33, 33, 33, 15, 3, 1, 1, 37, 37, 37, 37, 1, 1, 33] 201
rigid atoms, others: [32, 37, 38, 10, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042267 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042267
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042267/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042267
Building REAL300000042268
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042268'
/scratch/stefan/7769623/working/building/REAL300000042268 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042268

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042268/0 /scratch/stefan/7769623/working/building/REAL300000042268 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/298
`/scratch/stefan/7769623/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1Cl)

`REAL300000042268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042268 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 63, 63, 63, 63, 63, 63, 63, 63, 48, 48, 48, 11, 1, 1, 1, 1, 63, 63, 63] 63
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 108
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042268 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [9, 1, 9, 9, 36, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 63, 63, 63, 63, 1, 1, 1] 63
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 129
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042268 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042268
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042268/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042268
Building REAL300000042269
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042269'
/scratch/stefan/7769623/working/building/REAL300000042269 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042269

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042269/0 /scratch/stefan/7769623/working/building/REAL300000042269 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/299
`/scratch/stefan/7769623/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O)

`REAL300000042269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042269 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 25, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 4, 4, 4, 1, 1, 8, 25, 35, 35, 35, 35, 2] 70
rigid atoms, others: [1, 2, 3, 4, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 90
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042269 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 35, 35, 35, 35, 35, 24, 8, 1, 1, 1, 1, 70] 70
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 129
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042269 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042269/1 /scratch/stefan/7769623/working/building/REAL300000042269 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/300
`/scratch/stefan/7769623/working/3D/300' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1[O-])

`REAL300000042269.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042269/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042269 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 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: [4, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 13, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 5, 5, 5, 1, 1, 4, 13, 24, 24, 24, 24] 24
rigid atoms, others: [1, 2, 3, 4, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042269 none COC1=C([N+](=O)[O-])C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 24, 24, 24, 24, 24, 24, 21, 9, 1, 1, 1, 1] 24
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042269 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042269
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042269/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042269/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042269
Building REAL300000042270
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042270'
/scratch/stefan/7769623/working/building/REAL300000042270 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042270

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042270/0 /scratch/stefan/7769623/working/building/REAL300000042270 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/301
`/scratch/stefan/7769623/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(Cl)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042270 none COC(=O)C1=CC=C(Cl)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 51, 51, 51, 51, 51, 51, 51, 51, 1, 13, 13, 13, 1, 1, 8, 27, 51, 51, 51, 51, 1] 73
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 34, 22, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042270 none COC(=O)C1=CC=C(Cl)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 51, 73, 51, 51, 51, 51, 51, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 73, 73, 73, 51, 51, 28, 7, 1, 1, 1, 1, 51] 73
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042270 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042270
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042270/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042270
Building REAL300000042271
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042271'
/scratch/stefan/7769623/working/building/REAL300000042271 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042271

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042271/0 /scratch/stefan/7769623/working/building/REAL300000042271 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/302
`/scratch/stefan/7769623/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=COC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042271 none COC(=O)C1=COC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 88, 88, 160, 160, 160, 160, 160, 160, 160, 160, 1, 8, 8, 8, 1, 13, 13, 13, 13, 160, 160, 160, 160, 1] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 21, 25] set([0, 1, 3, 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: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042271 none COC(=O)C1=COC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 160, 201, 160, 160, 160, 51, 8, 51, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 160, 201, 201, 201, 160, 51, 51, 51, 51, 1, 1, 1, 1, 160] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 465
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042271 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042271/1 /scratch/stefan/7769623/working/building/REAL300000042271 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/303
`/scratch/stefan/7769623/working/3D/303' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=COC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042271.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042271/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042271 none COC(=O)C1=COC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 11, 11, 11, 32, 54, 54, 54, 54, 54, 54, 54, 54, 1, 11, 11, 11, 1, 12, 12, 12, 31, 54, 54, 54, 53, 1] 85
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 21, 25] set([0, 1, 3, 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: 142
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042271 none COC(=O)C1=COC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [84, 84, 53, 85, 53, 53, 53, 29, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 85, 85, 85, 53, 30, 30, 30, 8, 1, 1, 1, 1, 53] 85
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 223
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042271 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042271
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042271/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042271/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042271
Building REAL300000042272
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042272'
/scratch/stefan/7769623/working/building/REAL300000042272 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042272

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042272/0 /scratch/stefan/7769623/working/building/REAL300000042272 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/304
`/scratch/stefan/7769623/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1)

`REAL300000042272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042272 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 128, 128, 128, 128, 128, 201, 201, 201, 201, 201, 60, 60, 60, 60, 1, 1, 1, 1, 128, 128, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 514
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042272 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 60, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 201, 201, 201, 201, 13, 13, 1, 1] 201
rigid atoms, others: [34, 35, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 425
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042272 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H]1C1=CC=C(Cl)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 53, 53, 128, 128, 128, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 7, 7, 7, 128, 128, 128, 128, 1, 1, 13, 13] 201
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042272 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042272
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042272/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042272
Building REAL300000042273
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042273'
/scratch/stefan/7769623/working/building/REAL300000042273 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042273

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042273/0 /scratch/stefan/7769623/working/building/REAL300000042273 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/305
`/scratch/stefan/7769623/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21)

`REAL300000042273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042273 none CC(C)C1CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 5, 20, 20, 20, 20, 1, 1, 1, 1] 21
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 40, 41, 39, 17, 18, 19, 20, 21, 22, 38, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37])
total number of confs: 42
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042273 none CC(C)C1CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 20, 21, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 20, 20, 20, 7, 1, 1, 1, 1, 20, 20, 20, 20] 21
rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 42
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042273 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042273
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042273/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042273
Building REAL300000042274
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042274'
/scratch/stefan/7769623/working/building/REAL300000042274 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042274

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042274/0 /scratch/stefan/7769623/working/building/REAL300000042274 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/306
`/scratch/stefan/7769623/working/3D/306' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(=O)(=O)NC)=C1)

`REAL300000042274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042274 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(=O)(=O)NC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [27, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 40, 40, 16, 19, 40, 40, 53, 53, 53, 57, 40, 27, 27, 27, 27, 27, 4, 1, 1, 1, 1, 40, 40, 57, 57, 57, 57, 40] 60
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 272
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042274 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(=O)(=O)NC)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 1, 9, 9, 29, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 1, 23, 23, 23, 23, 23, 29, 40, 40, 40, 40, 1, 1, 9, 9, 9, 9, 1] 60
rigid atoms, others: [2, 36, 37, 42, 14, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41])
total number of confs: 182
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042274 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042274
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042274/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042274
Building REAL300000042275
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042275'
/scratch/stefan/7769623/working/building/REAL300000042275 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042275

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042275/0 /scratch/stefan/7769623/working/building/REAL300000042275 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/307
`/scratch/stefan/7769623/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CS1)

`REAL300000042275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042275 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 63, 63, 63, 63, 63, 41, 41, 41, 10, 1, 1, 1, 1, 63, 63] 63
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28])
total number of confs: 108
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042275 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Br)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [13, 1, 13, 13, 43, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 13, 13, 13, 43, 63, 63, 63, 63, 1, 1] 63
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 135
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042275 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042275
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042275/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042275
Building REAL300000042276
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042276'
/scratch/stefan/7769623/working/building/REAL300000042276 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042276

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042276/0 /scratch/stefan/7769623/working/building/REAL300000042276 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/308
`/scratch/stefan/7769623/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(N)(=O)=O)=C1)

`REAL300000042276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042276 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(N)(=O)=O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 129, 129, 32, 102, 129, 129, 137, 137, 137, 129, 69, 69, 69, 69, 69, 8, 1, 1, 1, 1, 129, 129, 137, 137, 129] 173
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 663
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042276 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(S(N)(=O)=O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 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: [33, 12, 1, 12, 12, 74, 129, 129, 129, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 33, 33, 33, 33, 33, 74, 129, 129, 129, 129, 1, 1, 4, 4, 1] 173
rigid atoms, others: [2, 35, 36, 39, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 374
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042276 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042276
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042276/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042276
Building REAL300000042277
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042277'
/scratch/stefan/7769623/working/building/REAL300000042277 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042277

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042277/0 /scratch/stefan/7769623/working/building/REAL300000042277 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/309
`/scratch/stefan/7769623/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CN1C=C(C(F)(F)F)C=CC1=O)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042277 none CC(CN1C=C(C(F)(F)F)C=CC1=O)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [24, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 24, 107, 107, 152, 152, 152, 152, 152, 152, 152, 152, 24, 24, 24, 24, 5, 5, 1, 1, 1, 152, 152, 152, 152] 152
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 10, 11, 12, 13, 31] set([0, 1, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 283
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042277 none CC(CN1C=C(C(F)(F)F)C=CC1=O)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [41, 8, 41, 118, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 118, 118, 152, 152, 152, 1, 1, 1, 1] 152
rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 507
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042277 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042277
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042277/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042277
Building REAL300000042278
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042278'
/scratch/stefan/7769623/working/building/REAL300000042278 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042278

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042278/0 /scratch/stefan/7769623/working/building/REAL300000042278 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/310
`/scratch/stefan/7769623/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N(CCN=NC1=CC=CC(C(=O)[O-])=C1)C(C)(C)C)

`REAL300000042278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042278 none CC(C)(C)OC(=O)N(CCN=NC1=CC=CC(C(=O)[O-])=C1)C(C)(C)C 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 179, 121, 179, 92, 58, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 121, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 58, 58, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 135, 135] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 805
number of broken/clashed sets: 172
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042278 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042278
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042278/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042278
Building REAL300000042279
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042279'
/scratch/stefan/7769623/working/building/REAL300000042279 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042279

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042279/0 /scratch/stefan/7769623/working/building/REAL300000042279 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/311
`/scratch/stefan/7769623/working/3D/311' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(CN=NC1=CC=CC(C(=O)[O-])=C1)CNC(=O)OC(C)(C)C)

`REAL300000042279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042279 none CC(C)C(CN=NC1=CC=CC(C(=O)[O-])=C1)CNC(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 52, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 59, 160, 193, 193, 201, 201, 201, 201, 52, 52, 52, 52, 52, 52, 52, 49, 23, 23, 1, 1, 1, 1, 59, 58, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 15, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 714
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042279 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042279
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042279/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042279
Building REAL300000042280
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042280'
/scratch/stefan/7769623/working/building/REAL300000042280 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042280

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042280/0 /scratch/stefan/7769623/working/building/REAL300000042280 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/312
`/scratch/stefan/7769623/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1)

`REAL300000042280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042280 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 37, 101, 101, 177, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 7, 7, 7, 1, 1, 1, 1, 1, 37, 37, 101, 177, 201, 201, 201, 201, 37] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 33, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 483
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042280 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [195, 87, 195, 201, 201, 195, 201, 201, 87, 87, 87, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 87, 195, 195, 195, 201, 201, 195, 201, 201, 87, 87, 30, 8, 1, 1, 1, 1, 87] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 475
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042280 none CN(C1=CC=CC=C1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 37, 37, 12, 37, 37, 1, 1, 1, 1, 1, 7, 7, 50, 88, 88, 88, 88, 88, 88, 88, 87, 1, 1, 12, 12, 12, 37, 37, 12, 37, 37, 1, 1, 7, 50, 88, 88, 88, 87, 1] 201
rigid atoms, others: [1, 34, 35, 8, 9, 10, 11, 12, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 278
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042280 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042280
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042280/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042280
Building REAL300000042281
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042281'
/scratch/stefan/7769623/working/building/REAL300000042281 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042281

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042281/0 /scratch/stefan/7769623/working/building/REAL300000042281 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/313
`/scratch/stefan/7769623/working/3D/313' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1)

`REAL300000042281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042281 none N#CCCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 9, 1, 1, 1, 1, 1, 10, 10, 37, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 6, 6, 2, 6, 6, 1, 18, 18, 9, 9, 1, 10, 37, 71, 71, 71, 71, 6, 6, 6, 6] 201
rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 26, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 222
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042281 none N#CCCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 29, 6, 6, 6, 6, 6, 18, 18, 63, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 6, 49, 49, 29, 29, 6, 18, 63, 104, 104, 104, 104, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 402
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042281 none N#CCCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=NC=C2)=N1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 166, 71, 71, 71, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 104, 104, 94, 104, 104, 71, 198, 198, 166, 166, 71, 29, 8, 1, 1, 1, 1, 104, 104, 104, 104] 201
rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 824
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042281 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042281
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042281/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042281
Building REAL300000042282
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042282'
/scratch/stefan/7769623/working/building/REAL300000042282 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042282

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042282/0 /scratch/stefan/7769623/working/building/REAL300000042282 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/314
`/scratch/stefan/7769623/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=C1)

`REAL300000042282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042282 none O=C([O-])C1=CC=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 110, 201, 201, 201, 201, 201, 201, 41, 1, 1, 1, 1, 41, 41, 41, 41, 201, 201, 201, 201, 201, 201, 201, 41, 41, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042282 none O=C([O-])C1=CC=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 174, 174, 47, 47, 47, 15, 3, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 47, 47, 47, 47, 3, 3, 1, 1, 1, 1, 1, 47, 47, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 336
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042282 none O=C([O-])C1=CC=CC(N=NC2CC(OCC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 13, 13, 1, 1, 1, 1, 1, 6, 22, 47, 47, 25, 47, 47, 1, 41, 41, 41, 41, 1, 1, 1, 1, 22, 22, 47, 47, 47, 47, 47, 1, 1, 41] 201
rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 39])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042282 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042282
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042282/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042282
Building REAL300000042283
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042283'
/scratch/stefan/7769623/working/building/REAL300000042283 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042283

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042283/0 /scratch/stefan/7769623/working/building/REAL300000042283 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/315
`/scratch/stefan/7769623/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1)

`REAL300000042283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042283 none N#CC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 39, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 11, 39, 45, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042283 none N#CC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [44, 44, 44, 44, 44, 45, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 45, 40, 12, 1, 1, 1, 1, 44] 45
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 29])
total number of confs: 81
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042283 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042283
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042283/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042283
Building REAL300000042284
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042284'
/scratch/stefan/7769623/working/building/REAL300000042284 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042284

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042284/0 /scratch/stefan/7769623/working/building/REAL300000042284 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/316
`/scratch/stefan/7769623/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042284 none CN1N=C(Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 8, 8, 42, 61, 61, 61, 61, 61, 62, 62, 61, 2, 2, 2, 1, 8, 42, 61, 61, 61, 61] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 146
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042284 none CN1N=C(Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [61, 61, 61, 61, 61, 61, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 62, 62, 62, 61, 43, 12, 1, 1, 1, 1] 62
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042284 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042284
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042284/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042284
Building REAL300000042285
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042285'
/scratch/stefan/7769623/working/building/REAL300000042285 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042285

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042285/0 /scratch/stefan/7769623/working/building/REAL300000042285 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/317
`/scratch/stefan/7769623/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1)

`REAL300000042285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042285 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 133, 133, 133, 133, 133, 137, 137, 133, 137, 137, 51, 51, 51, 10, 1, 1, 1, 1, 133, 133, 137, 137, 133, 137, 137] 137
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 217
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: REAL300000042285 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [25, 5, 25, 25, 81, 137, 137, 137, 137, 137, 137, 137, 137, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 81, 137, 137, 137, 137, 5, 5, 1, 1, 1, 1, 1] 137
rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 286
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042285 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 57, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 12, 12, 12, 57, 133, 133, 133, 133, 1, 1, 5, 5, 1, 5, 5] 137
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 255
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042285 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042285
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042285/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042285
Building REAL300000042286
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042286'
/scratch/stefan/7769623/working/building/REAL300000042286 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042286

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042286/0 /scratch/stefan/7769623/working/building/REAL300000042286 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/318
`/scratch/stefan/7769623/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(O)C=C(O)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O)

`REAL300000042286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042286 none CC1=C(O)C=C(O)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
536  conformations in input
total number of sets (complete confs): 536
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 58, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 2, 2, 2, 2, 1, 2, 12, 58, 67, 67, 67, 67, 2] 536
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 164
number of broken/clashed sets: 284
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042286 none CC1=C(O)C=C(O)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
3  hydrogens need rotated
536  conformations in input
total number of sets (complete confs): 536
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 37, 56, 67, 67, 67, 37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 67, 67, 67, 134, 67, 134, 37, 10, 1, 1, 1, 1, 134] 536
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 616
number of broken/clashed sets: 284
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042286 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042286
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042286/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042286
Building REAL300000042287
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042287'
/scratch/stefan/7769623/working/building/REAL300000042287 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042287

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042287/0 /scratch/stefan/7769623/working/building/REAL300000042287 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/319
`/scratch/stefan/7769623/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC([N+](=O)[O-])=CC=C21)

`REAL300000042287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042287 none CC1(C)CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC([N+](=O)[O-])=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 20, 20, 20, 20, 1, 1, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 40, 39, 16, 17, 18, 19, 22, 23, 24, 38, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37])
total number of confs: 49
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042287 none CC1(C)CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC([N+](=O)[O-])=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 1, 1, 1, 1, 20, 20, 20] 20
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 38
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042287 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042287
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042287/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042287
Building REAL300000042288
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042288'
/scratch/stefan/7769623/working/building/REAL300000042288 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042288

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042288/0 /scratch/stefan/7769623/working/building/REAL300000042288 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/320
`/scratch/stefan/7769623/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=C1)

`REAL300000042288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042288 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 16, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 7, 29, 107, 107, 107, 107, 107, 1, 3, 3, 3, 1, 1, 4, 16, 30, 30, 30, 30, 29, 29, 107, 107, 107, 107, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 45, 18, 19, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042288 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 107, 107, 107, 107, 107, 107, 141, 141, 176, 201, 201, 201, 201, 201, 201, 201, 201, 40, 8, 1, 1, 1, 1, 1, 1, 1, 107, 155, 155, 155, 93, 107, 141, 176, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 107] 201
rigid atoms, others: [41, 42, 43, 44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 589
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042288 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(OCC2=CC=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 30, 19, 30, 30, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 47, 113, 201, 201, 201, 201, 201, 30, 41, 41, 41, 30, 30, 18, 6, 1, 1, 1, 1, 113, 113, 201, 201, 201, 201, 30] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 561
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042288 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042288
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042288/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042288
Building REAL300000042289
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042289'
/scratch/stefan/7769623/working/building/REAL300000042289 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042289

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042289/0 /scratch/stefan/7769623/working/building/REAL300000042289 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/321
`/scratch/stefan/7769623/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042289 none COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 29, 29, 97, 141, 141, 141, 141, 141, 141, 141, 141, 4, 4, 4, 1, 1, 1, 1, 9, 9, 29, 97, 141, 141, 141, 141] 141
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042289 none COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 141, 136, 141, 141, 80, 80, 80, 80, 80, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 141, 141, 141, 141, 141, 141, 141, 80, 80, 33, 8, 1, 1, 1, 1] 141
rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 241
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042289 none COC1=CC=CC=C1N1N=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [19, 9, 9, 9, 2, 9, 9, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 80, 80, 80, 80, 80, 80, 80, 80, 19, 19, 19, 9, 8, 9, 9, 1, 1, 10, 40, 80, 80, 80, 80] 141
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042289 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042289
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042289/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042289
Building REAL300000042290
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042290'
/scratch/stefan/7769623/working/building/REAL300000042290 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042290

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042290/0 /scratch/stefan/7769623/working/building/REAL300000042290 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/322
`/scratch/stefan/7769623/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=C1)

`REAL300000042290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042290 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 30, 30, 52, 52, 52, 52, 52, 52, 52, 113, 176, 201, 201, 1, 1, 1, 1, 8, 30, 52, 52, 52, 176, 176, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 603
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042290 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 183, 112, 112, 81, 81, 81, 81, 81, 81, 81, 40, 9, 1, 1, 1, 1, 201, 201, 201, 201, 183, 112, 81, 81, 81, 9, 9, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39])
total number of confs: 507
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042290 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC=C2OCC2CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 81, 81, 52, 52, 52, 52, 25, 6, 1, 1, 1, 37, 37, 81, 81, 81, 81, 81, 52] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 356
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042290 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042290
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042290/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042290
Building REAL300000042291
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042291'
/scratch/stefan/7769623/working/building/REAL300000042291 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042291

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042291/0 /scratch/stefan/7769623/working/building/REAL300000042291 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/323
`/scratch/stefan/7769623/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1SC(C)(C)C)

`REAL300000042291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042291 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1SC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 50, 50, 34, 50, 50, 50, 53, 72, 72, 72, 21, 21, 21, 6, 1, 1, 1, 1, 50, 50, 50, 50, 72, 72, 72, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 256
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042291 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1SC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 30, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 9, 9, 9, 30, 50, 50, 50, 50, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 72
rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 127
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042291 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042291
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042291/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042291
Building REAL300000042292
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042292'
/scratch/stefan/7769623/working/building/REAL300000042292 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042292

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042292/0 /scratch/stefan/7769623/working/building/REAL300000042292 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/324
`/scratch/stefan/7769623/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC=C(C3OCCO3)S2)=C1)

`REAL300000042292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042292 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 111, 111, 111, 111, 201, 201, 201, 201, 111, 1, 1, 1, 1, 36, 37, 111, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042292 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 183, 183, 71, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 71, 71, 13, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 33])
total number of confs: 422
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042292 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 111, 110, 111, 111, 51, 51, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 111, 110, 111, 111, 8, 8, 1, 13, 13, 13, 13, 13, 111] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042292 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042292/1 /scratch/stefan/7769623/working/building/REAL300000042292 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/325
`/scratch/stefan/7769623/working/3D/325' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC=C(C3OCCO3)S2)=C1)

`REAL300000042292.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042292/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042292 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 52, 52, 89, 89, 89, 89, 201, 201, 201, 201, 89, 1, 1, 1, 1, 13, 52, 89, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 464
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042292 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 201, 201, 201, 169, 53, 52, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 169, 53, 13, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 33])
total number of confs: 478
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042292 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(C3OCCO3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 12, 5, 5, 12, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 89, 88, 89, 89, 40, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 89, 88, 89, 89, 40, 6, 1, 13, 13, 13, 13, 13, 89] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042292 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042292
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042292/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042292/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042292
Building REAL300000042293
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042293'
/scratch/stefan/7769623/working/building/REAL300000042293 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042293

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042293/0 /scratch/stefan/7769623/working/building/REAL300000042293 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/326
`/scratch/stefan/7769623/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C(F)(F)F)S2)=C1)

`REAL300000042293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042293 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 40, 40, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 11, 40, 63, 1] 63
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26])
total number of confs: 106
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042293 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 44, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 63, 63, 63, 63, 44, 9, 1, 63] 63
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042293 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042293
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042293/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042293
Building REAL300000042294
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042294'
/scratch/stefan/7769623/working/building/REAL300000042294 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042294

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042294/0 /scratch/stefan/7769623/working/building/REAL300000042294 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/327
`/scratch/stefan/7769623/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1SC(C)(C)C)

`REAL300000042294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042294 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1SC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 62, 62, 62, 38, 62, 62, 62, 67, 67, 67, 67, 24, 24, 24, 6, 1, 1, 1, 1, 62, 62, 62, 67, 67, 67, 67, 67, 67, 67, 67, 67] 67
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 202
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042294 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1SC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 14, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 28, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 9, 9, 9, 28, 62, 62, 62, 62, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 67
rigid atoms, others: [1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 139
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042294 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042294
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042294/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042294
Building REAL300000042295
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042295'
/scratch/stefan/7769623/working/building/REAL300000042295 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042295

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042295/0 /scratch/stefan/7769623/working/building/REAL300000042295 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/328
`/scratch/stefan/7769623/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042295 none CCC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 63, 125, 125, 125, 125, 125, 125, 125, 125, 6, 6, 6, 6, 6, 1, 1, 1, 9, 63, 125, 125, 125, 125] 175
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 251
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042295 none CCC1=CC=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 125, 125, 125, 89, 125, 125, 125, 65, 65, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 175, 175, 175, 175, 175, 125, 103, 125, 65, 12, 1, 1, 1, 1] 175
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 597
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042295 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042295
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042295/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042295
Building REAL300000042296
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042296'
/scratch/stefan/7769623/working/building/REAL300000042296 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042296

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042296/0 /scratch/stefan/7769623/working/building/REAL300000042296 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/329
`/scratch/stefan/7769623/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(S(N)(=O)=O)=C(C)C=C1C)

`REAL300000042296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042296 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(S(N)(=O)=O)=C(C)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [56, 57, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 57, 105, 105, 105, 114, 114, 114, 57, 89, 105, 105, 105, 57, 57, 57, 13, 1, 1, 1, 1, 105, 114, 114, 105, 105, 105, 105, 105, 105, 105] 114
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 488
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042296 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(S(N)(=O)=O)=C(C)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 39, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 39, 105, 105, 105, 105, 1, 4, 4, 2, 2, 2, 1, 2, 2, 2] 114
rigid atoms, others: [1, 33, 39, 13, 14, 15, 16, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42])
total number of confs: 215
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042296 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042296
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042296/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042296
Building REAL300000042297
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042297'
/scratch/stefan/7769623/working/building/REAL300000042297 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042297

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042297/0 /scratch/stefan/7769623/working/building/REAL300000042297 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/330
`/scratch/stefan/7769623/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC(C(=NNC2=CC=CC(C(=O)[O-])=C2)C2CC2)=CC=C1Cl)

`REAL300000042297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042297 none NS(=O)(=O)C1=CC(C(=NNC2=CC=CC(C(=O)[O-])=C2)C2CC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [4, 1, 4, 4, 1, 1, 1, 1, 12, 12, 61, 92, 92, 92, 92, 92, 92, 92, 92, 12, 25, 25, 1, 1, 1, 1, 4, 4, 1, 61, 92, 92, 92, 92, 25, 25, 25, 25, 25, 1, 1] 100
rigid atoms, others: [1, 4, 5, 6, 7, 40, 39, 22, 23, 24, 25, 28] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042297 none NS(=O)(=O)C1=CC(C(=NNC2=CC=CC(C(=O)[O-])=C2)C2CC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [31, 25, 31, 31, 25, 25, 6, 1, 6, 6, 27, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 25, 25, 6, 10, 31, 31, 25, 27, 62, 62, 62, 62, 1, 1, 1, 1, 1, 25, 25] 100
rigid atoms, others: [34, 35, 36, 37, 38, 7, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 203
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042297 none NS(=O)(=O)C1=CC(C(=NNC2=CC=CC(C(=O)[O-])=C2)C2CC2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 1, 1, 1, 16, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [96, 92, 96, 96, 92, 92, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 62, 62, 92, 92, 31, 55, 96, 96, 92, 8, 1, 1, 1, 1, 62, 62, 62, 62, 62, 92, 92] 100
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 412
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042297 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042297
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042297/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042297
Building REAL300000042298
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042298'
/scratch/stefan/7769623/working/building/REAL300000042298 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042298

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042298/0 /scratch/stefan/7769623/working/building/REAL300000042298 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/331
`/scratch/stefan/7769623/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br)

`REAL300000042298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042298 none CC1=NN(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 53, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 2, 2, 2, 2, 2, 2, 12, 53, 71, 71, 71, 71] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042298 none CC1=NN(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 45, 45, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 71, 71, 71, 71, 71, 71, 45, 13, 1, 1, 1, 1] 71
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042298 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042298
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042298/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042298
Building REAL300000042299
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042299'
/scratch/stefan/7769623/working/building/REAL300000042299 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042299

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042299/0 /scratch/stefan/7769623/working/building/REAL300000042299 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/332
`/scratch/stefan/7769623/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=C1)

`REAL300000042299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042299 none O=C([O-])C1=CC=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 163, 163, 163, 163, 163, 175, 175, 163, 175, 175, 1, 1, 1, 1, 60, 61, 163, 163, 175, 175, 175, 175, 175, 1] 175
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 415
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: REAL300000042299 none O=C([O-])C1=CC=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 108, 108, 23, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 23, 23, 6, 6, 1, 1, 1, 1, 1, 175] 175
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 298
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042299 none O=C([O-])C1=CC=CC(N=NCC2=NC=CN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [163, 163, 163, 163, 162, 163, 163, 61, 61, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 163, 162, 163, 163, 7, 7, 1, 1, 6, 6, 2, 6, 6, 163] 175
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 255
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042299 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042299/1 /scratch/stefan/7769623/working/building/REAL300000042299 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/333
`/scratch/stefan/7769623/working/3D/333' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=C1)

`REAL300000042299.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042299/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042299 none O=C([O-])C1=CC=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 68, 68, 187, 187, 187, 187, 187, 194, 194, 187, 194, 194, 1, 1, 1, 1, 13, 68, 187, 187, 194, 194, 190, 194, 194, 1] 194
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 298
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: REAL300000042299 none O=C([O-])C1=CC=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 194, 194, 194, 194, 194, 137, 32, 32, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 137, 32, 6, 6, 1, 1, 1, 1, 1, 194] 194
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 426
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042299 none O=C([O-])C1=CC=CC(NN=CC2=NC=CN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [187, 187, 187, 187, 186, 187, 187, 99, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 187, 186, 187, 187, 99, 12, 1, 1, 6, 6, 1, 6, 6, 187] 194
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 378
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042299 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042299
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042299/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042299/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042299
Building REAL300000042300
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042300'
/scratch/stefan/7769623/working/building/REAL300000042300 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042300

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042300/0 /scratch/stefan/7769623/working/building/REAL300000042300 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/334
`/scratch/stefan/7769623/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CN1C)

`REAL300000042300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042300 none COC(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 29, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 13, 13, 13, 1, 6, 28, 53, 53, 53, 52, 1, 2, 2, 2] 83
rigid atoms, others: [32, 2, 4, 5, 6, 7, 19, 20, 21, 25] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042300 none COC(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [82, 82, 52, 82, 52, 52, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 52, 53, 83, 83, 83, 52, 28, 8, 1, 1, 1, 1, 53, 53, 53, 53] 83
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 208
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042300 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042300
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042300/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042300
Building REAL300000042301
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042301'
/scratch/stefan/7769623/working/building/REAL300000042301 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042301

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042301/0 /scratch/stefan/7769623/working/building/REAL300000042301 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/335
`/scratch/stefan/7769623/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(Br)=CC=C21)

`REAL300000042301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042301 none CC1(C)CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(Br)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 15, 15, 15, 15, 1, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 36, 38, 29, 30, 37] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 38
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042301 none CC1(C)CC(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(Br)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 15, 15, 15] 15
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 31
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042301 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042301
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042301/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042301
Building REAL300000042302
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042302'
/scratch/stefan/7769623/working/building/REAL300000042302 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042302

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042302/0 /scratch/stefan/7769623/working/building/REAL300000042302 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/336
`/scratch/stefan/7769623/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1C)

`REAL300000042302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042302 none COC(=O)CC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 10, 43, 1, 1, 1, 1, 1, 1, 8, 8, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 43, 43, 43, 10, 10, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 1, 2, 2, 2] 138
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 37, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042302 none COC(=O)CC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 92, 138, 41, 41, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 138, 138, 138, 92, 92, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 41, 41, 41, 41] 138
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 499
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042302 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042302
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042302/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042302
Building REAL300000042303
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042303'
/scratch/stefan/7769623/working/building/REAL300000042303 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042303

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042303/0 /scratch/stefan/7769623/working/building/REAL300000042303 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/337
`/scratch/stefan/7769623/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=N1)

`REAL300000042303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042303 none CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 2, 1, 12, 12, 69, 113, 113, 113, 113, 113, 113, 113, 113, 3, 3, 1, 1, 2, 2, 2, 1, 3, 3, 12, 69, 113, 113, 113, 113, 3, 3, 1] 113
rigid atoms, others: [0, 1, 2, 3, 4, 38, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042303 none CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 101, 99, 112, 112, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 112, 112, 113, 113, 113, 113, 113, 113, 112, 112, 60, 12, 1, 1, 1, 1, 112, 112, 113] 113
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 244
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042303 none CN1C=C(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 113, 113, 113, 113, 113, 113, 113, 113, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 7, 50, 113, 113, 113, 112, 1, 1, 3] 113
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 36, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042303 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042303
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042303/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042303
Building REAL300000042304
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042304'
/scratch/stefan/7769623/working/building/REAL300000042304 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042304

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042304/0 /scratch/stefan/7769623/working/building/REAL300000042304 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/338
`/scratch/stefan/7769623/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=C1)

`REAL300000042304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042304 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 7, 23, 23, 40, 40, 40, 40, 169, 201, 201, 201, 201, 201, 40, 1, 1, 1, 1, 7, 23, 40, 40, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042304 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 201, 201, 201, 201, 186, 125, 125, 74, 74, 74, 74, 11, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 186, 125, 74, 74, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042304 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(SC3=CC=CC=N3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [40, 40, 40, 40, 40, 40, 40, 20, 6, 6, 1, 1, 1, 1, 1, 1, 13, 74, 74, 74, 74, 74, 1, 40, 40, 40, 40, 20, 6, 1, 1, 74, 74, 74, 74, 40] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042304 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042304
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042304/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042304
Building REAL300000042305
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042305'
/scratch/stefan/7769623/working/building/REAL300000042305 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042305

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042305/0 /scratch/stefan/7769623/working/building/REAL300000042305 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/339
`/scratch/stefan/7769623/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC=C2Br)=C1)

`REAL300000042305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042305 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 44, 44, 74, 74, 74, 44, 74, 74, 74, 1, 1, 1, 1, 13, 44, 74, 74, 74, 1] 74
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042305 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 50, 9, 1, 1, 1, 74] 74
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 164
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042305 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042305
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042305/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042305
Building REAL300000042306
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042306'
/scratch/stefan/7769623/working/building/REAL300000042306 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042306

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042306/0 /scratch/stefan/7769623/working/building/REAL300000042306 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/340
`/scratch/stefan/7769623/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C=C1OC)C(=NNC1=CC=CC(C(=O)[O-])=C1)CC2)

`REAL300000042306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042306 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=CC(C(=O)[O-])=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 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, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 9, 57, 57, 57, 57, 57, 58, 58, 57, 1, 1, 4, 4, 4, 1, 1, 4, 4, 4, 9, 57, 57, 57, 57, 1, 1, 1, 1] 77
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 10, 11, 12, 40, 22, 23, 39, 27, 28, 37] set([0, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 88
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042306 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=CC(C(=O)[O-])=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 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, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 57, 57, 57, 57, 57, 57, 57, 57, 77, 57, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 57, 57, 77, 77, 77, 57, 57, 77, 77, 77, 10, 1, 1, 1, 1, 57, 57, 57, 57] 77
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042306 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042306
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042306/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042306
Building REAL300000042307
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042307'
/scratch/stefan/7769623/working/building/REAL300000042307 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042307

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042307/0 /scratch/stefan/7769623/working/building/REAL300000042307 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/341
`/scratch/stefan/7769623/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1)

`REAL300000042307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042307 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 84, 84, 84, 135, 135, 199, 201, 201, 201, 84, 47, 47, 47, 47, 1, 1, 1, 1, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 84] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 582
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042307 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 37, 37, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 7, 7, 14, 18, 18, 18, 1, 7, 7, 7, 7, 84, 84, 84, 84, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 45, 44, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042307 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042307
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042307/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042307
Building REAL300000042308
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042308'
/scratch/stefan/7769623/working/building/REAL300000042308 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042308

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042308/0 /scratch/stefan/7769623/working/building/REAL300000042308 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/342
`/scratch/stefan/7769623/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C(F)(F)F)=C1)

`REAL300000042308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042308 none CN(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 15, 15, 15, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 32, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 32, 99, 99, 99, 99, 1] 102
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 39, 19, 20, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 178
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042308 none CN(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 15, 15, 15, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 87, 102, 59, 99, 99, 59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 99, 99, 99, 99, 99, 99, 102, 102, 102, 102, 102, 102, 99, 99, 59, 12, 1, 1, 1, 1, 99] 102
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 370
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042308 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042308
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042308/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042308
Building REAL300000042309
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042309'
/scratch/stefan/7769623/working/building/REAL300000042309 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042309

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042309/0 /scratch/stefan/7769623/working/building/REAL300000042309 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/343
`/scratch/stefan/7769623/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=C1)

`REAL300000042309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042309 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 153, 153, 153, 153, 153, 161, 161, 161, 161, 161, 1, 1, 1, 1, 13, 72, 153, 153, 161, 161, 153, 161, 161, 1] 161
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 239
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: REAL300000042309 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 161, 161, 161, 161, 161, 161, 106, 22, 22, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 106, 22, 5, 5, 1, 1, 1, 1, 1, 161] 161
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 342
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042309 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [153, 153, 153, 153, 153, 153, 153, 72, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 153, 153, 153, 153, 72, 11, 1, 1, 5, 5, 1, 5, 5, 153] 161
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 299
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042309 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042309
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042309/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042309
Building REAL300000042310
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042310'
/scratch/stefan/7769623/working/building/REAL300000042310 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042310

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042310/0 /scratch/stefan/7769623/working/building/REAL300000042310 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/344
`/scratch/stefan/7769623/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC2=CC=C(Br)C=C2C(=NNC2=CC=CC(C(=O)[O-])=C2)C1)

`REAL300000042310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042310 none CC1CCC2=CC=C(Br)C=C2C(=NNC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 22, 22, 21, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 1, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41] set([35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042310 none CC1CCC2=CC=C(Br)C=C2C(=NNC2=CC=CC(C(=O)[O-])=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 22, 22, 22, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 21, 21] 22
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042310 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042310
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042310/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042310
Building REAL300000042311
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042311'
/scratch/stefan/7769623/working/building/REAL300000042311 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042311

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042311/0 /scratch/stefan/7769623/working/building/REAL300000042311 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/345
`/scratch/stefan/7769623/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C=C2C(F)(F)F)=C1)

`REAL300000042311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042311 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 41, 41, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 13, 41, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042311 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 51, 51, 51, 51, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 51, 51, 51, 51, 30, 5, 1, 1, 1, 51] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042311 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042311
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042311/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042311
Building REAL300000042312
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042312'
/scratch/stefan/7769623/working/building/REAL300000042312 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042312

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042312/0 /scratch/stefan/7769623/working/building/REAL300000042312 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/346
`/scratch/stefan/7769623/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(C)C(C)N=NC2=CC=CC(C(=O)[O-])=C2)C=C1OC)

`REAL300000042312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042312 none COC1=CC=C(C(C)C(C)N=NC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 65, 65, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5, 15, 16, 16, 16, 155, 155, 155, 155, 1, 3, 3, 3] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 21, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042312 none COC1=CC=C(C(C)C(C)N=NC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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, 155, 155, 155, 155, 93, 46, 93, 8, 46, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 155, 155, 155, 201, 201, 201, 201, 155, 155, 93, 93, 93, 93, 46, 46, 46, 46, 1, 1, 1, 1, 155, 201, 201, 201] 201
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 673
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042312 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042312
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042312/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042312
Building REAL300000042313
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042313'
/scratch/stefan/7769623/working/building/REAL300000042313 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042313

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042313/0 /scratch/stefan/7769623/working/building/REAL300000042313 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/347
`/scratch/stefan/7769623/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C(C)C1=CC=C(Cl)C=C1)

`REAL300000042313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042313 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C(C)C1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 102, 107, 107, 107, 107, 107, 107, 107, 51, 51, 51, 51, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107] 107
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 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: 431
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042313 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C(C)C1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 1, 1, 16, 1, 1, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 62, 62, 107, 107, 107, 107, 107, 107, 107, 107, 1, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 107, 107, 107, 107, 4, 4, 4, 4, 1, 1, 1, 1] 107
rigid atoms, others: [34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 187
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042313 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042313
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042313/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042313
Building REAL300000042314
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042314'
/scratch/stefan/7769623/working/building/REAL300000042314 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042314

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042314/0 /scratch/stefan/7769623/working/building/REAL300000042314 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/348
`/scratch/stefan/7769623/working/3D/348' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=CC2=C1C(=NNC1=CC=CC(C(=O)[O-])=C1)CC2)

`REAL300000042314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042314 none CC1=CC(Br)=CC2=C1C(=NNC1=CC=CC(C(=O)[O-])=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 23, 23, 22, 1, 1, 2, 2, 2, 1, 1, 9, 22, 22, 22, 22, 1, 1, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 32, 20, 21, 25, 26, 35] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042314 none CC1=CC(Br)=CC2=C1C(=NNC1=CC=CC(C(=O)[O-])=C1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 23, 23, 23, 22, 22, 8, 1, 1, 1, 1, 22, 22, 22, 22] 23
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 49
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042314 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042314
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042314/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042314
Building REAL300000042315
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042315'
/scratch/stefan/7769623/working/building/REAL300000042315 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042315

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042315/0 /scratch/stefan/7769623/working/building/REAL300000042315 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/349
`/scratch/stefan/7769623/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)C(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042315 none COC1=CC=C2C(=C1)C(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 27, 27, 27, 27] 27
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 27, 28, 29, 37] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42])
total number of confs: 58
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042315 none COC1=CC=C2C(=C1)C(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1] 27
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 47
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042315 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042315
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042315/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042315
Building REAL300000042316
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042316'
/scratch/stefan/7769623/working/building/REAL300000042316 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042316

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042316/0 /scratch/stefan/7769623/working/building/REAL300000042316 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/350
`/scratch/stefan/7769623/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1O)

`REAL300000042316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042316 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 69, 69, 69, 67, 69, 69, 69, 69, 37, 37, 37, 10, 1, 1, 1, 1, 69, 69, 138] 138
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 270
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042316 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 43, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 43, 69, 69, 69, 69, 1, 1, 2] 138
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 157
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042316 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042316/1 /scratch/stefan/7769623/working/building/REAL300000042316 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/351
`/scratch/stefan/7769623/working/3D/351' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1[O-])

`REAL300000042316.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042316/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042316 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 21, 21] 21
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 40
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042316 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=C(Cl)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 1, 1] 21
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042316 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042316
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042316/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042316/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042316
Building REAL300000042317
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042317'
/scratch/stefan/7769623/working/building/REAL300000042317 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042317

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042317/0 /scratch/stefan/7769623/working/building/REAL300000042317 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/352
`/scratch/stefan/7769623/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1)

`REAL300000042317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042317 none CC(C)N(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 12, 39, 1, 12, 1, 1, 1, 1, 1, 6, 6, 40, 72, 72, 72, 72, 72, 72, 72, 71, 1, 1, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 1, 1, 6, 40, 72, 72, 72, 71, 1] 201
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 21, 22, 41] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 282
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042317 none CC(C)N(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 71, 201, 71, 71, 71, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71, 24, 6, 1, 1, 1, 1, 71] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 462
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042317 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042317
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042317/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042317
Building REAL300000042318
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042318'
/scratch/stefan/7769623/working/building/REAL300000042318 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042318

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042318/0 /scratch/stefan/7769623/working/building/REAL300000042318 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/353
`/scratch/stefan/7769623/working/3D/353' -> `0.mol2'
Preparing input files

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

`REAL300000042318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042318 none O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 61, 61, 57, 59, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 13, 50, 61, 61, 61, 1] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042318 none O=C([O-])C1=CC=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 36, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 61, 61, 61, 61, 36, 7, 1, 1, 1, 61] 61
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042318 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042318
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042318/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042318
Building REAL300000042319
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042319'
/scratch/stefan/7769623/working/building/REAL300000042319 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042319

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042319/0 /scratch/stefan/7769623/working/building/REAL300000042319 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/354
`/scratch/stefan/7769623/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C(Cl)=C2)=C1)

`REAL300000042319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042319 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 45, 45, 70, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 13, 45, 71, 71, 71, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 124
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042319 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 51, 9, 1, 1, 1, 71] 71
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 155
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042319 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042319
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042319/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042319
Building REAL300000042320
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042320'
/scratch/stefan/7769623/working/building/REAL300000042320 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042320

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042320/0 /scratch/stefan/7769623/working/building/REAL300000042320 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/355
`/scratch/stefan/7769623/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCN(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1)

`REAL300000042320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042320 none COCCN(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 39, 25, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 22, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 57, 57, 57, 39, 39, 25, 25, 10, 10, 10, 1, 1, 6, 21, 37, 37, 37, 36, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 22, 23, 42] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 275
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042320 none COCCN(C)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 162, 108, 36, 108, 36, 36, 36, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 201, 201, 201, 201, 201, 162, 162, 108, 108, 108, 36, 36, 14, 4, 1, 1, 1, 1, 37] 201
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 792
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042320 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042320
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042320/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042320
Building REAL300000042321
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042321'
/scratch/stefan/7769623/working/building/REAL300000042321 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042321

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042321/0 /scratch/stefan/7769623/working/building/REAL300000042321 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/356
`/scratch/stefan/7769623/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC(Cl)=C2F)=C1)

`REAL300000042321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042321 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC(Cl)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
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, 1, 1, 1, 1, 13, 36, 36, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 13, 36, 132, 66, 66, 1] 132
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 243
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042321 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC(Cl)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 56, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 56, 13, 2, 1, 1, 66] 132
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 155
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042321 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042321/1 /scratch/stefan/7769623/working/building/REAL300000042321 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/357
`/scratch/stefan/7769623/working/3D/357' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C([O-])C=CC(Cl)=C2F)=C1)

`REAL300000042321.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042321/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042321 none O=C([O-])C1=CC=CC(NN=CC2=C([O-])C=CC(Cl)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 4, 12, 12, 12, 1] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 20
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042321 none O=C([O-])C1=CC=CC(NN=CC2=C([O-])C=CC(Cl)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 6, 1, 1, 12] 12
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042321 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042321
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042321/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042321/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042321
Building REAL300000042322
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042322'
/scratch/stefan/7769623/working/building/REAL300000042322 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042322

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042322/0 /scratch/stefan/7769623/working/building/REAL300000042322 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/358
`/scratch/stefan/7769623/working/3D/358' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1[N+](=O)[O-])

`REAL300000042322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042322 none COC(=O)COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 21, 39, 5, 1, 1, 1, 1, 1, 1, 9, 9, 37, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 2, 2, 40, 40, 40, 21, 21, 1, 1, 9, 37, 68, 68, 68, 68, 1] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 40, 22, 23, 24] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 265
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042322 none COC(=O)COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 201, 134, 36, 44, 68, 68, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 68, 68, 68, 68, 201, 201, 201, 199, 199, 68, 68, 34, 8, 1, 1, 1, 1, 68] 201
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 647
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042322 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042322
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042322/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042322
Building REAL300000042323
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042323'
/scratch/stefan/7769623/working/building/REAL300000042323 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042323

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042323/0 /scratch/stefan/7769623/working/building/REAL300000042323 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/359
`/scratch/stefan/7769623/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=C1)

`REAL300000042323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042323 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 13, 55, 55, 100, 100, 100, 102, 102, 100, 102, 102, 102, 102, 102, 102, 100, 100, 1, 1, 1, 1, 13, 55, 100, 102, 102, 102, 102, 100, 1] 102
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([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: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042323 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 102, 102, 102, 69, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 102, 102, 102, 102, 69, 18, 4, 1, 1, 1, 1, 4, 102] 102
rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 223
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042323 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(C(F)(F)F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [100, 100, 100, 100, 100, 100, 100, 45, 7, 7, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 4, 4, 1, 1, 100, 100, 100, 100, 44, 7, 1, 4, 4, 4, 4, 1, 100] 102
rigid atoms, others: [32, 37, 10, 11, 12, 13, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 38])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042323 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042323
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042323/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042323
Building REAL300000042324
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042324'
/scratch/stefan/7769623/working/building/REAL300000042324 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042324

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042324/0 /scratch/stefan/7769623/working/building/REAL300000042324 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/360
`/scratch/stefan/7769623/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)C(=O)[O-])

`REAL300000042324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042324 none CC(OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 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: [24, 7, 1, 1, 1, 1, 1, 1, 7, 7, 41, 74, 75, 74, 74, 74, 75, 75, 74, 1, 1, 24, 31, 31, 24, 24, 24, 24, 1, 1, 7, 41, 75, 75, 74, 74, 1, 1] 172
rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 255
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042324 none CC(OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 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, 136, 75, 46, 75, 75, 26, 25, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 75, 172, 172, 172, 172, 172, 172, 172, 75, 74, 25, 6, 1, 1, 1, 1, 75, 75] 172
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 545
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042324 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042324
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042324/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042324
Building REAL300000042325
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042325'
/scratch/stefan/7769623/working/building/REAL300000042325 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042325

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042325/0 /scratch/stefan/7769623/working/building/REAL300000042325 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/361
`/scratch/stefan/7769623/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2C3=CC=CC=C3CC23CCOCC3)=C1)

`REAL300000042325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042325 none O=C([O-])C1=CC=CC(NN=C2C3=CC=CC=C3CC23CCOCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 25
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042325 none O=C([O-])C1=CC=CC(NN=C2C3=CC=CC=C3CC23CCOCC3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 43, 24, 25, 26, 27, 28])
total number of confs: 23
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042325 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042325
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042325/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042325
Building REAL300000042326
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042326'
/scratch/stefan/7769623/working/building/REAL300000042326 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042326

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042326/0 /scratch/stefan/7769623/working/building/REAL300000042326 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/362
`/scratch/stefan/7769623/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1)

`REAL300000042326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042326 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 63, 63, 63, 63, 63, 78, 78, 78, 78, 63, 30, 30, 30, 8, 1, 1, 1, 1, 63, 63, 63, 78, 78, 63] 78
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 134
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: REAL300000042326 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [20, 5, 20, 20, 64, 78, 78, 78, 78, 78, 78, 78, 78, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 64, 78, 78, 78, 78, 5, 5, 5, 1, 1, 5] 78
rigid atoms, others: [35, 36, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37])
total number of confs: 183
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042326 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 43, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 11, 43, 63, 63, 63, 63, 1, 1, 1, 5, 5, 1] 78
rigid atoms, others: [32, 1, 34, 37, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 144
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042326 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042326
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042326/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042326
Building REAL300000042327
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042327'
/scratch/stefan/7769623/working/building/REAL300000042327 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042327

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042327/0 /scratch/stefan/7769623/working/building/REAL300000042327 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/363
`/scratch/stefan/7769623/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(F)(F)F)C=C1)

`REAL300000042327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042327 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 23, 23, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 91, 91, 26, 30, 160, 174, 178, 178, 91, 91, 45, 45, 45, 44, 44, 4, 1, 1, 1, 1, 91, 91, 91, 91] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 628
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042327 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 1, 7, 7, 37, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 12, 23, 23, 23, 1, 1, 15, 15, 15, 15, 15, 37, 91, 91, 91, 91, 1, 1, 1, 1] 201
rigid atoms, others: [2, 35, 36, 37, 38, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 278
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042327 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042327
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042327/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042327
Building REAL300000042328
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042328'
/scratch/stefan/7769623/working/building/REAL300000042328 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042328

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042328/0 /scratch/stefan/7769623/working/building/REAL300000042328 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/364
`/scratch/stefan/7769623/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2)C(N)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042328 none CC1=NN(C2=CC=CC=C2)C(N)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 1, 10, 10, 53, 115, 115, 115, 115, 115, 115, 115, 115, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 10, 53, 115, 115, 115, 115] 201
rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 243
number of broken/clashed sets: 103
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042328 none CC1=NN(C2=CC=CC=C2)C(N)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 115, 115, 201, 201, 201, 201, 201, 115, 115, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 115, 115, 115, 201, 201, 201, 201, 201, 115, 115, 63, 12, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 347
number of broken/clashed sets: 103
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042328 none CC1=NN(C2=CC=CC=C2)C(N)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 37, 37, 144, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 37, 144, 201, 201, 201, 201] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 441
number of broken/clashed sets: 103
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042328 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042328
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042328/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042328
Building REAL300000042329
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042329'
/scratch/stefan/7769623/working/building/REAL300000042329 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042329

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042329/0 /scratch/stefan/7769623/working/building/REAL300000042329 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/365
`/scratch/stefan/7769623/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=C(Cl)C=C2)=C1)

`REAL300000042329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042329 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 24, 25, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 50
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: REAL300000042329 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 13, 13, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 20] 20
rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 32
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042329 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 20] 20
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 40, 41, 42, 43, 44])
total number of confs: 30
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042329 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042329
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042329/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042329
Building REAL300000042330
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042330'
/scratch/stefan/7769623/working/building/REAL300000042330 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042330

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042330/0 /scratch/stefan/7769623/working/building/REAL300000042330 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/366
`/scratch/stefan/7769623/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(CS(=O)(=O)N(C)C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042330 none CC(C)C(CS(=O)(=O)N(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [96, 48, 100, 8, 48, 91, 153, 153, 153, 156, 156, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 101, 101, 101, 101, 101, 101, 48, 91, 91, 156, 156, 156, 156, 156, 156, 1, 1, 1, 1] 171
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 957
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042330 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042330
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042330/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042330
Building REAL300000042331
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042331'
/scratch/stefan/7769623/working/building/REAL300000042331 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042331

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042331/0 /scratch/stefan/7769623/working/building/REAL300000042331 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/367
`/scratch/stefan/7769623/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2CCC2=O)=C1)

`REAL300000042331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042331 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2CCC2=O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 95, 95, 95, 95, 95, 126, 126, 126, 126, 95, 33, 33, 33, 8, 1, 1, 1, 1, 95, 95, 95, 126, 126, 126, 126, 95] 126
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 206
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: REAL300000042331 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2CCC2=O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 7, 32, 32, 99, 126, 126, 126, 126, 126, 126, 126, 126, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 99, 126, 126, 126, 126, 6, 7, 7, 1, 1, 1, 1, 7] 126
rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 299
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042331 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2CCC2=O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 57, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 7, 6, 7, 7, 1, 11, 11, 11, 57, 95, 95, 95, 95, 1, 1, 1, 7, 7, 7, 7, 1] 126
rigid atoms, others: [32, 1, 34, 33, 39, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 207
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042331 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042331
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042331/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042331
Building REAL300000042332
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042332'
/scratch/stefan/7769623/working/building/REAL300000042332 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042332

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042332/0 /scratch/stefan/7769623/working/building/REAL300000042332 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/368
`/scratch/stefan/7769623/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F)

`REAL300000042332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042332 none NS(=O)(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 1, 5, 5, 1, 1, 1, 1, 9, 9, 56, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 5, 5, 1, 9, 56, 97, 97, 97, 97, 1, 1] 184
rigid atoms, others: [32, 1, 4, 5, 6, 7, 19, 20, 21, 22, 25, 33] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042332 none NS(=O)(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 97, 184, 184, 97, 97, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 97, 97, 79, 81, 184, 184, 97, 55, 12, 1, 1, 1, 1, 97, 97] 184
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 587
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042332 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042332
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042332/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042332
Building REAL300000042333
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042333'
/scratch/stefan/7769623/working/building/REAL300000042333 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042333

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042333/0 /scratch/stefan/7769623/working/building/REAL300000042333 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/369
`/scratch/stefan/7769623/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1N1C=CN=N1)

`REAL300000042333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042333 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1N1C=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 73, 73, 46, 73, 73, 73, 85, 85, 85, 85, 32, 32, 32, 7, 1, 1, 1, 1, 73, 73, 73, 73, 85, 85] 85
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 245
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042333 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1N1C=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [25, 11, 25, 25, 66, 85, 85, 85, 85, 85, 85, 85, 85, 11, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 25, 25, 25, 66, 85, 85, 85, 85, 11, 11, 11, 11, 1, 1] 85
rigid atoms, others: [36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 207
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042333 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1N1C=CN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 9, 37, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 9, 9, 9, 37, 73, 73, 73, 73, 1, 1, 1, 1, 11, 11] 85
rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 153
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042333 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042333
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042333/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042333
Building REAL300000042334
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042334'
/scratch/stefan/7769623/working/building/REAL300000042334 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042334

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042334/0 /scratch/stefan/7769623/working/building/REAL300000042334 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/370
`/scratch/stefan/7769623/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1)

`REAL300000042334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042334 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 45, 45, 100, 100, 100, 100, 100, 100, 100, 100, 100, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 45, 100, 100, 100, 100, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 47, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 623
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042334 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 144, 51, 51, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 144, 51, 11, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47])
total number of confs: 475
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042334 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 100, 99, 100, 100, 42, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 100, 99, 100, 100, 42, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 100] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 205
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042334 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042334/1 /scratch/stefan/7769623/working/building/REAL300000042334 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/371
`/scratch/stefan/7769623/working/3D/371' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N[NH+]=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1)

`REAL300000042334.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042334/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042334 none O=C([O-])C1=CC=CC(N[NH+]=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 20, 20, 20, 95, 95, 95, 95, 95, 95, 95, 95, 95, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 12, 20, 95, 95, 95, 95, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 48, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 629
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: REAL300000042334 none O=C([O-])C1=CC=CC(N[NH+]=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 102, 92, 92, 92, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 102, 92, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48])
total number of confs: 398
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042334 none O=C([O-])C1=CC=CC(N[NH+]=CC2=CC=C3C(=C2)CCN3CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 22, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 95, 95, 95, 95, 22, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 95] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 174
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042334 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042334
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042334/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042334/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042334
Building REAL300000042335
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042335'
/scratch/stefan/7769623/working/building/REAL300000042335 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042335

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042335/0 /scratch/stefan/7769623/working/building/REAL300000042335 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/372
`/scratch/stefan/7769623/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2NC(=O)COC2=C1)

`REAL300000042335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042335 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2NC(=O)COC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 46, 46, 46, 10, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86] 86
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 144
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042335 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2NC(=O)COC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 51, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 51, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1] 86
rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 183
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042335 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042335
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042335/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042335
Building REAL300000042336
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042336'
/scratch/stefan/7769623/working/building/REAL300000042336 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042336

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042336/0 /scratch/stefan/7769623/working/building/REAL300000042336 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/373
`/scratch/stefan/7769623/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OC1=CC=CC=C1)

`REAL300000042336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042336 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 51, 51, 52, 52, 52, 52, 52, 52, 1, 1, 1, 7, 22, 22, 7, 22, 22, 2, 2, 2, 2, 2, 2, 1, 52, 52, 52, 52, 1, 1, 1, 22, 22, 7, 22, 22] 110
rigid atoms, others: [0, 1, 2, 3, 4, 37, 15, 16, 17, 35, 36, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 38, 39, 40, 41, 42])
total number of confs: 130
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: REAL300000042336 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 79, 79, 110, 110, 110, 110, 110, 110, 110, 110, 22, 7, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 110, 110, 110, 110, 22, 22, 22, 1, 1, 1, 1, 1] 110
rigid atoms, others: [38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 185
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042336 none CC1(C)C(N=NC2=CC=CC(C(=O)[O-])=C2)CC1OC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 108, 110, 110, 108, 110, 110, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 52, 52, 52, 110, 110, 108, 110, 110] 110
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 210
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042336 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042336
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042336/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042336
Building REAL300000042337
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042337'
/scratch/stefan/7769623/working/building/REAL300000042337 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042337

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042337/0 /scratch/stefan/7769623/working/building/REAL300000042337 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/374
`/scratch/stefan/7769623/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1)

`REAL300000042337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042337 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 8, 8, 42, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2, 1, 1, 8, 42, 69, 69, 69, 69, 1] 81
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 141
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042337 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 49, 48, 69, 69, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 69, 69, 69, 81, 81, 81, 69, 69, 48, 12, 1, 1, 1, 1, 69] 81
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042337 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042337
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042337/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042337
Building REAL300000042338
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042338'
/scratch/stefan/7769623/working/building/REAL300000042338 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042338

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042338/0 /scratch/stefan/7769623/working/building/REAL300000042338 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/375
`/scratch/stefan/7769623/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042338 none CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 8, 26, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 4, 4, 4, 4, 8, 26, 33, 33, 33, 33] 33
rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
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: REAL300000042338 none CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 33, 33, 33, 33, 33, 22, 6, 1, 1, 1, 1] 33
rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 55
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042338 none CC1=NN(C2=CC=CC=N2)C(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 28, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 1, 1, 1, 1, 13, 28, 33, 33, 33, 33] 33
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042338 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042338
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042338/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042338
Building REAL300000042339
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042339'
/scratch/stefan/7769623/working/building/REAL300000042339 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042339

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042339/0 /scratch/stefan/7769623/working/building/REAL300000042339 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/376
`/scratch/stefan/7769623/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(CC(C)C)=C1)

`REAL300000042339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042339 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(CC(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 119, 119, 119, 119, 119, 196, 201, 201, 119, 32, 32, 32, 8, 1, 1, 1, 1, 119, 119, 119, 196, 196, 201, 201, 201, 201, 201, 201, 201, 119] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 618
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042339 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(CC(C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 56, 119, 119, 119, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 4, 5, 7, 1, 11, 11, 11, 56, 119, 119, 119, 119, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 1] 201
rigid atoms, others: [32, 1, 33, 43, 13, 14, 15, 16, 17, 18, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 276
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042339 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042339
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042339/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042339
Building REAL300000042340
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042340'
/scratch/stefan/7769623/working/building/REAL300000042340 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042340

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042340/0 /scratch/stefan/7769623/working/building/REAL300000042340 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/377
`/scratch/stefan/7769623/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C)C=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042340 none COC1=C(C)C=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 75, 180, 180, 180, 180, 180, 180, 180, 180, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 13, 13, 13, 75, 180, 180, 180, 180, 1] 180
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 38, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 345
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042340 none COC1=C(C)C=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [180, 180, 180, 180, 180, 180, 54, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 55, 55, 55, 10, 1, 1, 1, 1, 180] 180
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 251
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042340 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042340
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042340/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042340
Building REAL300000042341
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042341'
/scratch/stefan/7769623/working/building/REAL300000042341 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042341

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042341/0 /scratch/stefan/7769623/working/building/REAL300000042341 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/378
`/scratch/stefan/7769623/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=C(C)NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042341 none CCOC(=O)C1=C(C)NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [44, 24, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 31, 82, 82, 82, 82, 82, 82, 82, 82, 1, 45, 45, 45, 44, 44, 2, 2, 2, 1, 7, 31, 82, 82, 82, 82, 1] 198
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 38, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 296
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042341 none CCOC(=O)C1=C(C)NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 186, 180, 82, 180, 82, 82, 82, 82, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 198, 198, 198, 198, 198, 82, 82, 82, 82, 50, 10, 1, 1, 1, 1, 82] 198
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 513
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042341 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042341
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042341/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042341
Building REAL300000042342
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042342'
/scratch/stefan/7769623/working/building/REAL300000042342 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042342

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042342/0 /scratch/stefan/7769623/working/building/REAL300000042342 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/379
`/scratch/stefan/7769623/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(C)(C)C1=CNC2=CC=CC=C12)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042342 none CC(CC(C)(C)C1=CNC2=CC=CC=C12)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [22, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 80, 80, 134, 134, 134, 134, 134, 134, 134, 134, 22, 22, 22, 22, 18, 18, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134] 134
rigid atoms, others: [3, 6, 38, 7, 8, 9, 10, 39, 12, 13, 14, 11, 40, 43, 41, 42] set([0, 1, 2, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47])
total number of confs: 269
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042342 none CC(CC(C)(C)C1=CNC2=CC=CC=C12)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [37, 8, 37, 47, 106, 106, 106, 134, 134, 134, 134, 134, 134, 134, 134, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 47, 47, 106, 106, 106, 106, 106, 106, 134, 134, 134, 134, 134, 134, 1, 1, 1, 1] 134
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 478
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042342 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042342
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042342/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042342
Building REAL300000042343
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042343'
/scratch/stefan/7769623/working/building/REAL300000042343 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042343

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042343/0 /scratch/stefan/7769623/working/building/REAL300000042343 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/380
`/scratch/stefan/7769623/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CSC=C2Br)=C1)

`REAL300000042343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042343 none O=C([O-])C1=CC=CC(NN=CC2=CSC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 43, 43, 43, 43, 43, 1, 1, 1, 1, 11, 35, 43, 43, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24])
total number of confs: 68
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042343 none O=C([O-])C1=CC=CC(NN=CC2=CSC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 32, 10, 1, 1, 43] 43
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042343 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042343
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042343/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042343
Building REAL300000042344
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042344'
/scratch/stefan/7769623/working/building/REAL300000042344 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042344

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042344/0 /scratch/stefan/7769623/working/building/REAL300000042344 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/381
`/scratch/stefan/7769623/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCOC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042344 none CCCCOC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 13, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 47, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 24, 24, 24, 23, 23, 13, 13, 5, 5, 1, 1, 11, 11, 11, 47, 73, 73, 73, 73, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 43, 44, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 273
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042344 none CCCCOC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 119, 112, 46, 46, 73, 73, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 119, 119, 73, 73, 19, 19, 19, 4, 1, 1, 1, 1, 73, 73] 201
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 743
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042344 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042344
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042344/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042344
Building REAL300000042345
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042345'
/scratch/stefan/7769623/working/building/REAL300000042345 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042345

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042345/0 /scratch/stefan/7769623/working/building/REAL300000042345 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/382
`/scratch/stefan/7769623/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(I)=C2)=C1)

`REAL300000042345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042345 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(I)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 65, 65, 63, 65, 65, 65, 1, 1, 1, 1, 13, 37, 65, 65, 65, 65, 1] 65
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042345 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(I)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 64, 65, 65, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 65, 64, 65, 65, 46, 10, 1, 1, 1, 1, 65] 65
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042345 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042345
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042345/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042345
Building REAL300000042346
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042346'
/scratch/stefan/7769623/working/building/REAL300000042346 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042346

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042346/0 /scratch/stefan/7769623/working/building/REAL300000042346 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/383
`/scratch/stefan/7769623/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CSC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042346 none COC(=O)C1=CSC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 13, 13, 13, 53, 95, 95, 95, 95, 95, 95, 95, 95, 1, 12, 12, 12, 1, 13, 13, 13, 53, 95, 95, 95, 95, 1] 133
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 21, 25] set([0, 1, 3, 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: 223
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042346 none COC(=O)C1=CSC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 95, 133, 95, 95, 95, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 95, 133, 133, 133, 95, 36, 36, 36, 7, 1, 1, 1, 1, 95] 133
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 296
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042346 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042346
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042346/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042346
Building REAL300000042347
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042347'
/scratch/stefan/7769623/working/building/REAL300000042347 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042347

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042347/0 /scratch/stefan/7769623/working/building/REAL300000042347 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/384
`/scratch/stefan/7769623/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCOC3=CC(F)=CC=C32)=C1)

`REAL300000042347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042347 none O=C([O-])C1=CC=CC(NN=C2CCOC3=CC(F)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 37
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042347 none O=C([O-])C1=CC=CC(NN=C2CCOC3=CC(F)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 33])
total number of confs: 35
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042347 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042347
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042347/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042347
Building REAL300000042348
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042348'
/scratch/stefan/7769623/working/building/REAL300000042348 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042348

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042348/0 /scratch/stefan/7769623/working/building/REAL300000042348 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/385
`/scratch/stefan/7769623/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=C(Br)S1)

`REAL300000042348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042348 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=C(Br)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 62, 62, 62, 62, 62, 62, 39, 39, 39, 10, 1, 1, 1, 1, 63, 63, 63, 63] 63
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 119
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042348 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=C(Br)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 44, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 43, 63, 63, 63, 62, 1, 2, 2, 2] 63
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31])
total number of confs: 159
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042348 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042348
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042348/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042348
Building REAL300000042349
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042349'
/scratch/stefan/7769623/working/building/REAL300000042349 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042349

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042349/0 /scratch/stefan/7769623/working/building/REAL300000042349 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/386
`/scratch/stefan/7769623/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(F)C(F)=C2)=C1)

`REAL300000042349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042349 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(F)C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 48, 135, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 47, 48, 135, 135, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042349 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(F)C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 138, 138, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 40, 40, 7, 7, 1, 1, 1, 201] 201
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042349 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042349
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042349/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042349
Building REAL300000042350
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042350'
/scratch/stefan/7769623/working/building/REAL300000042350 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042350

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042350/0 /scratch/stefan/7769623/working/building/REAL300000042350 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/387
`/scratch/stefan/7769623/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC=C2OC(F)(F)F)=C1)

`REAL300000042350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042350 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC=C2OC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 80, 80, 80, 27, 80, 80, 80, 134, 134, 134, 134, 1, 1, 1, 1, 8, 27, 80, 79, 80, 1] 134
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042350 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC=C2OC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [80, 80, 80, 80, 80, 80, 80, 46, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 80, 80, 80, 80, 46, 12, 1, 1, 1, 80] 134
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042350 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042350
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042350/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042350
Building REAL300000042351
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042351'
/scratch/stefan/7769623/working/building/REAL300000042351 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042351

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042351/0 /scratch/stefan/7769623/working/building/REAL300000042351 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/388
`/scratch/stefan/7769623/working/3D/388' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=C1)

`REAL300000042351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042351 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 13, 49, 49, 59, 59, 49, 49, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 13, 49, 59, 59, 59, 59, 59, 59, 59, 59, 1] 59
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042351 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 59, 37, 7, 7, 2, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 59, 59, 59, 59, 37, 7, 3, 3, 1, 1, 1, 1, 3, 3, 59] 59
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 126
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042351 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(Cl)C=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 59, 26, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 59, 59, 59, 59, 26, 4, 1, 1, 3, 3, 3, 3, 1, 1, 59] 59
rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042351 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042351
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042351/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042351
Building REAL300000042352
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042352'
/scratch/stefan/7769623/working/building/REAL300000042352 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042352

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042352/0 /scratch/stefan/7769623/working/building/REAL300000042352 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/389
`/scratch/stefan/7769623/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC(C(F)(F)F)=C2)=C1)

`REAL300000042352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042352 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 23, 32, 32, 28, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 32, 32, 28, 32, 1] 32
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 79
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: REAL300000042352 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 20, 20, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32, 32, 32, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 32] 32
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 55
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042352 none O=C([O-])C1=CC=CC(N=NC2CCCC2C2=CC=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 23] 32
rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41])
total number of confs: 41
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042352 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042352
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042352/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042352
Building REAL300000042353
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042353'
/scratch/stefan/7769623/working/building/REAL300000042353 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042353

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042353/0 /scratch/stefan/7769623/working/building/REAL300000042353 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/390
`/scratch/stefan/7769623/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21)

`REAL300000042353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042353 none O=C([O-])CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 3
rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 36, 27, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 14
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042353 none O=C([O-])CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 3, 3, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 3
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 34, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 36])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042353 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042353
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042353/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042353
Building REAL300000042354
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042354'
/scratch/stefan/7769623/working/building/REAL300000042354 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042354

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042354/0 /scratch/stefan/7769623/working/building/REAL300000042354 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/391
`/scratch/stefan/7769623/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1O)

`REAL300000042354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042354 none CC1=C(C)C(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 53, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 53, 67, 67, 67, 67, 2, 2, 2, 2] 268
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 176
number of broken/clashed sets: 202
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042354 none CC1=C(C)C(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 134, 39, 9, 1, 1, 1, 1, 67, 67, 67, 134] 268
rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 373
number of broken/clashed sets: 202
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042354 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042354
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042354/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042354
Building REAL300000042355
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042355'
/scratch/stefan/7769623/working/building/REAL300000042355 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042355

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042355/0 /scratch/stefan/7769623/working/building/REAL300000042355 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/392
`/scratch/stefan/7769623/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=C1)

`REAL300000042355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042355 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 13, 50, 87, 87, 87, 87, 87, 1] 87
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
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: REAL300000042355 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 71, 23, 23, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 87, 87, 87, 87, 71, 23, 4, 1, 1, 1, 1, 87] 87
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 201
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042355 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=C(Cl)C=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 52, 11, 11, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 87, 87, 87, 87, 52, 11, 1, 4, 4, 4, 4, 87] 87
rigid atoms, others: [10, 11, 12, 13, 14, 15, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 186
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042355 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042355
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042355/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042355
Building REAL300000042356
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042356'
/scratch/stefan/7769623/working/building/REAL300000042356 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042356

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042356/0 /scratch/stefan/7769623/working/building/REAL300000042356 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/393
`/scratch/stefan/7769623/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C)C(Cl)=C1)

`REAL300000042356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042356 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 16, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 130, 130, 93, 130, 201, 201, 201, 130, 130, 130, 31, 31, 31, 6, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 201, 201, 130] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 502
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042356 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 16, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 52, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 5, 11, 11, 1, 1, 1, 9, 9, 9, 52, 130, 130, 130, 130, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1] 201
rigid atoms, others: [32, 1, 33, 41, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 276
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042356 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042356
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042356/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042356
Building REAL300000042357
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042357'
/scratch/stefan/7769623/working/building/REAL300000042357 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042357

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042357/0 /scratch/stefan/7769623/working/building/REAL300000042357 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/394
`/scratch/stefan/7769623/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1)

`REAL300000042357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042357 none COC(=O)C1=C(C)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 24, 40, 40, 40, 40, 40, 40, 40, 40, 1, 12, 12, 12, 2, 2, 2, 1, 6, 23, 40, 40, 40, 39, 1] 61
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 21, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042357 none COC(=O)C1=C(C)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 60, 39, 60, 39, 39, 40, 39, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 61, 61, 61, 40, 40, 40, 40, 27, 8, 1, 1, 1, 1, 39] 61
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042357 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042357
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042357/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042357
Building REAL300000042358
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042358'
/scratch/stefan/7769623/working/building/REAL300000042358 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042358

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042358/0 /scratch/stefan/7769623/working/building/REAL300000042358 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/395
`/scratch/stefan/7769623/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C)N(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042358 none COC(=O)C1=C(C)N(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 47, 72, 72, 72, 72, 72, 72, 72, 72, 1, 13, 13, 13, 2, 2, 2, 2, 2, 2, 12, 47, 72, 72, 72, 72, 1] 124
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 22, 38] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042358 none COC(=O)C1=C(C)N(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [124, 124, 72, 124, 72, 72, 72, 72, 72, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 72, 124, 124, 124, 72, 72, 72, 72, 72, 72, 30, 8, 1, 1, 1, 1, 72] 124
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042358 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042358
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042358/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042358
Building REAL300000042359
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042359'
/scratch/stefan/7769623/working/building/REAL300000042359 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042359

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042359/0 /scratch/stefan/7769623/working/building/REAL300000042359 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/396
`/scratch/stefan/7769623/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1)

`REAL300000042359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042359 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 40, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 12, 12, 12, 1, 1, 8, 40, 66, 66, 66, 66, 1] 106
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042359 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 61, 106, 60, 66, 66, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 106, 106, 106, 66, 66, 46, 10, 1, 1, 1, 1, 66] 106
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 281
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042359 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042359
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042359/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042359
Building REAL300000042360
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042360'
/scratch/stefan/7769623/working/building/REAL300000042360 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042360

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042360/0 /scratch/stefan/7769623/working/building/REAL300000042360 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/397
`/scratch/stefan/7769623/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=C1)

`REAL300000042360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042360 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 49, 49, 85, 85, 85, 85, 186, 201, 201, 197, 201, 201, 85, 85, 1, 1, 1, 1, 11, 49, 186, 186, 201, 201, 201, 201, 201, 85, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 645
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042360 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 143, 53, 53, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 143, 53, 5, 5, 1, 1, 1, 1, 1, 16, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 473
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042360 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N(CC3=CC=CC=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 33, 6, 6, 1, 1, 1, 1, 1, 1, 8, 16, 16, 10, 16, 16, 1, 1, 85, 85, 85, 85, 33, 6, 8, 8, 16, 16, 16, 16, 16, 1, 85] 201
rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042360 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042360
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042360/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042360
Building REAL300000042361
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042361'
/scratch/stefan/7769623/working/building/REAL300000042361 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042361

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042361/0 /scratch/stefan/7769623/working/building/REAL300000042361 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/398
`/scratch/stefan/7769623/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042361 none COC1=NC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 113, 113, 113, 113, 113, 113, 113, 113, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 63, 113, 113, 113, 113, 1] 113
rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 244
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042361 none COC1=NC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 113, 45, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 113, 113, 113, 113, 113, 113, 113, 46, 46, 46, 10, 1, 1, 1, 1, 113] 113
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 179
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042361 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042361
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042361/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042361
Building REAL300000042362
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042362'
/scratch/stefan/7769623/working/building/REAL300000042362 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042362

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042362/0 /scratch/stefan/7769623/working/building/REAL300000042362 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/399
`/scratch/stefan/7769623/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CCC1)

`REAL300000042362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042362 none CC(C)(C)OC(=O)N1CCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [22, 18, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1] 121
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45])
total number of confs: 123
number of broken/clashed sets: 121
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042362 none CC(C)(C)OC(=O)N1CCCC(N=NC2=CC=CC(C(=O)[O-])=C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 121, 91, 46, 91, 46, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 46, 121, 121, 121, 121, 121, 121, 121, 121, 121, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46] 121
rigid atoms, others: [45, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51])
total number of confs: 307
number of broken/clashed sets: 121
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042362 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042362
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042362/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042362
Building REAL300000042363
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042363'
/scratch/stefan/7769623/working/building/REAL300000042363 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042363

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042363/0 /scratch/stefan/7769623/working/building/REAL300000042363 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/400
`/scratch/stefan/7769623/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC(C(F)(F)F)=C32)=CC=C1)

`REAL300000042363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042363 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC(C(F)(F)F)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 11, 19, 19, 19, 19, 1, 1, 1] 20
rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 22, 23, 24, 25, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042363 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC(C(F)(F)F)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 19, 20, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 7, 1, 1, 1, 1, 19, 19, 19] 20
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 33, 22, 23, 24, 25, 26, 31])
total number of confs: 36
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042363 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042363
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042363/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042363
Building REAL300000042364
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042364'
/scratch/stefan/7769623/working/building/REAL300000042364 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042364

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042364/0 /scratch/stefan/7769623/working/building/REAL300000042364 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/401
`/scratch/stefan/7769623/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC(F)=C(F)C(F)=C32)=C1)

`REAL300000042364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042364 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(F)=C(F)C(F)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 9, 26, 26, 26, 26, 26, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042364 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(F)=C(F)C(F)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 26] 26
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23, 24, 25, 26])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042364 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042364
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042364/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042364
Building REAL300000042365
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042365'
/scratch/stefan/7769623/working/building/REAL300000042365 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042365

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042365/0 /scratch/stefan/7769623/working/building/REAL300000042365 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/402
`/scratch/stefan/7769623/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042365 none CC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 39, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 10, 39, 50, 50, 50, 50, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 119
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042365 none CC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 50, 50, 50, 50, 50, 50, 37, 11, 1, 1, 1, 1, 50] 50
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042365 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042365
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042365/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042365
Building REAL300000042366
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042366'
/scratch/stefan/7769623/working/building/REAL300000042366 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042366

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042366/0 /scratch/stefan/7769623/working/building/REAL300000042366 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/403
`/scratch/stefan/7769623/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=C1)

`REAL300000042366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042366 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 66, 66, 134, 134, 134, 134, 174, 174, 174, 174, 174, 174, 174, 134, 1, 1, 1, 1, 13, 66, 134, 174, 174, 174, 1] 174
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042366 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 174, 174, 174, 174, 174, 174, 131, 44, 44, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 174, 174, 174, 174, 131, 44, 11, 1, 1, 1, 174] 174
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 388
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042366 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=C(F)C=CC=C3F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [134, 134, 134, 134, 134, 134, 134, 56, 10, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 134, 134, 134, 134, 56, 10, 1, 7, 7, 7, 134] 174
rigid atoms, others: [10, 11, 12, 13, 14, 15, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042366 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042366
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042366/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042366
Building REAL300000042367
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042367'
/scratch/stefan/7769623/working/building/REAL300000042367 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042367

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042367/0 /scratch/stefan/7769623/working/building/REAL300000042367 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/404
`/scratch/stefan/7769623/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2F)=C1)

`REAL300000042367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042367 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 11, 30, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042367 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 26, 9, 1, 1, 1, 35] 35
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042367 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042367
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042367/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042367
Building REAL300000042368
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042368'
/scratch/stefan/7769623/working/building/REAL300000042368 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042368

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042368/0 /scratch/stefan/7769623/working/building/REAL300000042368 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/405
`/scratch/stefan/7769623/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=C(Cl)C=C2)=C1)

`REAL300000042368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042368 none O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 41, 41, 41, 41, 41, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 63, 63, 63, 63, 63, 63, 1] 63
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 204
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: REAL300000042368 none O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 38, 38, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 63] 63
rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 104
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042368 none O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 5, 5, 8, 8, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 41] 63
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 83
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042368 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042368
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042368/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042368
Building REAL300000042369
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042369'
/scratch/stefan/7769623/working/building/REAL300000042369 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042369

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042369/0 /scratch/stefan/7769623/working/building/REAL300000042369 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/406
`/scratch/stefan/7769623/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C(I)=C1)

`REAL300000042369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042369 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C(I)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 102, 102, 94, 100, 102, 102, 102, 52, 52, 52, 10, 1, 1, 1, 1, 102, 102, 102] 102
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 202
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042369 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C(I)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 62, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 102, 102, 102, 102, 1, 1, 1] 102
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 213
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042369 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042369
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042369/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042369
Building REAL300000042370
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042370'
/scratch/stefan/7769623/working/building/REAL300000042370 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042370

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042370/0 /scratch/stefan/7769623/working/building/REAL300000042370 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/407
`/scratch/stefan/7769623/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C=C1F)C(=NNC1=CC=CC(C(=O)[O-])=C1)C(=O)N2)

`REAL300000042370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042370 none COC1=CC2=C(C=C1F)C(=NNC1=CC=CC(C(=O)[O-])=C1)C(=O)N2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 37, 37, 38, 38, 37, 1, 1, 1, 4, 4, 4, 1, 1, 7, 37, 37, 37, 37, 1] 38
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 21, 22, 23, 27, 28] set([0, 32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042370 none COC1=CC2=C(C=C1F)C(=NNC1=CC=CC(C(=O)[O-])=C1)C(=O)N2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 38, 38, 38, 37, 37, 11, 1, 1, 1, 1, 37] 38
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042370 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042370
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042370/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042370
Building REAL300000042371
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042371'
/scratch/stefan/7769623/working/building/REAL300000042371 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042371

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042371/0 /scratch/stefan/7769623/working/building/REAL300000042371 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/408
`/scratch/stefan/7769623/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)OC2=CC=CC=C21)

`REAL300000042371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042371 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)OC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 92, 92, 92, 92, 92, 92, 92, 92, 92, 42, 42, 42, 10, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92] 92
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 153
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042371 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)OC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 47, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 92, 92, 92, 92, 2, 2, 2, 1, 1, 1, 1] 92
rigid atoms, others: [1, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 190
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042371 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042371
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042371/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042371
Building REAL300000042372
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042372'
/scratch/stefan/7769623/working/building/REAL300000042372 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042372

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042372/0 /scratch/stefan/7769623/working/building/REAL300000042372 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/409
`/scratch/stefan/7769623/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC12CCC(CC1N=NC1=CC=CC(C(=O)[O-])=C1)C2(C)C)

`REAL300000042372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042372 none CC(C)(C)OC(=O)NC12CCC(CC1N=NC1=CC=CC(C(=O)[O-])=C1)C2(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [12, 9, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2] 48
rigid atoms, others: [45, 11, 38, 7, 8, 9, 10, 39, 12, 13, 14, 44, 40, 43, 41, 25, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55])
total number of confs: 76
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042372 none CC(C)(C)OC(=O)NC12CCC(CC1N=NC1=CC=CC(C(=O)[O-])=C1)C2(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 37, 26, 37, 26, 26, 26, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26] 48
rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53, 54, 55])
total number of confs: 124
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042372 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042372
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042372/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042372
Building REAL300000042373
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042373'
/scratch/stefan/7769623/working/building/REAL300000042373 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042373

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042373/0 /scratch/stefan/7769623/working/building/REAL300000042373 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/410
`/scratch/stefan/7769623/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCCC2CC(N=NC3=CC=CC(C(=O)[O-])=C3)CCC21)

`REAL300000042373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042373 none CC(C)(C)OC(=O)N1CCCC2CC(N=NC3=CC=CC(C(=O)[O-])=C3)CCC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 19, 26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 1, 1, 1, 1, 1] 173
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50])
total number of confs: 131
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042373 none CC(C)(C)OC(=O)N1CCCC2CC(N=NC3=CC=CC(C(=O)[O-])=C3)CCC21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [173, 173, 173, 173, 103, 49, 103, 49, 49, 49, 49, 49, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 173, 173, 173, 173, 173, 173, 173, 173, 173, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 49, 49, 49, 49, 49] 173
rigid atoms, others: [48, 49, 50, 47, 16, 17, 18, 19, 20, 21, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54, 55])
total number of confs: 394
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042373 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042373
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042373/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042373
Building REAL300000042374
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042374'
/scratch/stefan/7769623/working/building/REAL300000042374 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042374

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042374/0 /scratch/stefan/7769623/working/building/REAL300000042374 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/411
`/scratch/stefan/7769623/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCN1C(=O)OC(C)(C)C)

`REAL300000042374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042374 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [41, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 47, 47, 47, 47, 47, 47, 87, 87, 141, 143, 143, 143, 41, 41, 41, 41, 41, 29, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 143, 143, 143, 143, 143, 143, 143, 143, 143] 143
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 13, 36] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 481
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042374 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 1, 4, 18, 18, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 17, 17, 17, 7, 7, 7, 7, 7, 4, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 143
rigid atoms, others: [2, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 122
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042374 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042374
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042374/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042374
Building REAL300000042375
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042375'
/scratch/stefan/7769623/working/building/REAL300000042375 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042375

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042375/0 /scratch/stefan/7769623/working/building/REAL300000042375 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/412
`/scratch/stefan/7769623/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(SC2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042375 none COC1=CC=CC(SC2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 45, 45, 45, 45, 45, 45, 92, 92, 142, 201, 201, 201, 201, 201, 201, 201, 201, 1, 3, 3, 3, 1, 1, 1, 45, 45, 45, 45, 92, 142, 201, 201, 201, 201, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 486
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042375 none COC1=CC=CC(SC2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 93, 40, 40, 40, 25, 40, 40, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 40, 22, 8, 1, 1, 1, 1, 201] 201
rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 341
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042375 none COC1=CC=CC(SC2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 45, 45, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 40, 40, 40, 40, 40, 40, 40, 40, 45, 70, 70, 70, 45, 45, 45, 1, 1, 1, 1, 6, 23, 40, 40, 40, 40, 45] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 182
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042375 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042375
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042375/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042375
Building REAL300000042376
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042376'
/scratch/stefan/7769623/working/building/REAL300000042376 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042376

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042376/0 /scratch/stefan/7769623/working/building/REAL300000042376 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/413
`/scratch/stefan/7769623/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(CCC3=CC=CC=C3)S2)=C1)

`REAL300000042376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042376 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(CCC3=CC=CC=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 46, 46, 78, 78, 78, 78, 180, 201, 201, 201, 201, 201, 201, 78, 1, 1, 1, 1, 11, 46, 78, 180, 180, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 676
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042376 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(CCC3=CC=CC=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 153, 58, 58, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 153, 58, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40])
total number of confs: 470
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042376 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(CCC3=CC=CC=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 38, 7, 7, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 1, 78, 78, 78, 78, 38, 7, 1, 8, 8, 15, 14, 15, 15, 14, 15, 15, 78] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042376 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042376
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042376/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042376
Building REAL300000042377
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042377'
/scratch/stefan/7769623/working/building/REAL300000042377 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042377

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042377/0 /scratch/stefan/7769623/working/building/REAL300000042377 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/414
`/scratch/stefan/7769623/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC(=O)OC(C)(C)C)N=N1)

`REAL300000042377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042377 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC(=O)OC(C)(C)C)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 8, 8, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 38, 38, 38, 97, 197, 197, 201, 201, 201, 201, 38, 38, 15, 15, 15, 15, 1, 1, 1, 1, 38, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042377 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC(=O)OC(C)(C)C)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 8, 8, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 28, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 8, 52, 52, 57, 57, 57, 57, 1, 1, 7, 7, 7, 7, 38, 38, 38, 38, 1, 8, 8, 57, 57, 57, 57, 57, 57, 57, 57, 57] 201
rigid atoms, others: [1, 34, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042377 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042377
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042377/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042377
Building REAL300000042378
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042378'
/scratch/stefan/7769623/working/building/REAL300000042378 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042378

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042378/0 /scratch/stefan/7769623/working/building/REAL300000042378 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/415
`/scratch/stefan/7769623/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=CC(Cl)=CN=C3O2)=C1)

`REAL300000042378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042378 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC(Cl)=CN=C3O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 11, 36, 42, 42, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042378 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC(Cl)=CN=C3O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 42, 41, 42, 42, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 41, 42, 42, 29, 6, 1, 1, 1, 42] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042378 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042378
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042378/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042378
Building REAL300000042379
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042379'
/scratch/stefan/7769623/working/building/REAL300000042379 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042379

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042379/0 /scratch/stefan/7769623/working/building/REAL300000042379 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/416
`/scratch/stefan/7769623/working/3D/416' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC=C3F)S2)=C1)

`REAL300000042379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042379 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC=C3F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47, 88, 88, 88, 88, 201, 201, 121, 201, 201, 201, 88, 1, 1, 1, 1, 11, 47, 88, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 592
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042379 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC=C3F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 161, 47, 47, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 160, 46, 12, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 462
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042379 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC=C3F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 37, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 13, 1, 88, 88, 88, 88, 36, 8, 1, 12, 12, 12, 12, 88] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042379 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042379
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042379/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042379
Building REAL300000042380
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042380'
/scratch/stefan/7769623/working/building/REAL300000042380 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042380

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042380/0 /scratch/stefan/7769623/working/building/REAL300000042380 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/417
`/scratch/stefan/7769623/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2Br)=C1)

`REAL300000042380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042380 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 11, 29, 29, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 11, 29, 38, 38, 38, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 65
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042380 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 27, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 27, 10, 1, 1, 1, 38] 38
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 83
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042380 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042380
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042380/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042380
Building REAL300000042381
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042381'
/scratch/stefan/7769623/working/building/REAL300000042381 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042381

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042381/0 /scratch/stefan/7769623/working/building/REAL300000042381 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/418
`/scratch/stefan/7769623/working/3D/418' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=CC=CC=C2C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042381 none COC1=CC2=CC=CC=C2C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 78, 78, 78, 78, 78, 78, 78, 78, 4, 4, 4, 1, 1, 1, 1, 1, 1, 11, 43, 78, 78, 78, 78] 78
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30, 31] set([0, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042381 none COC1=CC2=CC=CC=C2C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 78, 78, 78, 78, 78, 78, 78, 57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 57, 12, 1, 1, 1, 1] 78
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042381 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042381
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042381/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042381
Building REAL300000042382
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042382'
/scratch/stefan/7769623/working/building/REAL300000042382 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042382

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042382/0 /scratch/stefan/7769623/working/building/REAL300000042382 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/419
`/scratch/stefan/7769623/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(N2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=N2)C=C1)

`REAL300000042382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042382 none COC1=CC=C(N2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 73, 90, 90, 90, 90, 90, 90, 90, 90, 6, 6, 1, 1, 2, 2, 2, 1, 1, 6, 25, 72, 90, 90, 90, 90, 6, 1, 1] 90
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 23, 24, 38, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042382 none COC1=CC=C(N2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 86, 86, 86, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 86, 86, 90, 90, 90, 90, 90, 90, 90, 86, 37, 8, 1, 1, 1, 1, 86, 90, 90] 90
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 143
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042382 none COC1=CC=C(N2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 2, 6, 6, 1, 1, 1, 1, 1, 10, 10, 46, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 6, 6, 7, 7, 7, 6, 6, 1, 10, 46, 86, 86, 86, 86, 1, 6, 6] 90
rigid atoms, others: [5, 6, 7, 8, 9, 21, 22, 30, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042382 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042382
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042382/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042382
Building REAL300000042383
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042383'
/scratch/stefan/7769623/working/building/REAL300000042383 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042383

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042383/0 /scratch/stefan/7769623/working/building/REAL300000042383 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/420
`/scratch/stefan/7769623/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C)

`REAL300000042383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042383 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 50, 50, 50, 50, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 123, 123, 123] 123
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 270
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: REAL300000042383 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 4, 24, 87, 87, 123, 123, 123, 123, 123, 123, 123, 123, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 24, 24, 24, 24, 123, 123, 123, 123, 4, 1, 1, 1, 1, 1, 4, 4, 4] 123
rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 223
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042383 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 54, 54, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 9, 9, 9, 9, 123, 123, 123, 123, 1, 4, 4, 1, 4, 4, 2, 2, 2] 123
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 197
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042383 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042383/1 /scratch/stefan/7769623/working/building/REAL300000042383 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/421
`/scratch/stefan/7769623/working/3D/421' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C)

`REAL300000042383.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042383/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042383 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 59, 59, 59, 59, 60, 60, 59, 60, 60, 59, 59, 41, 41, 41, 12, 1, 1, 1, 1, 59, 60, 60, 59, 60, 60, 60, 60, 60] 60
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 120
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: REAL300000042383 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [15, 4, 15, 15, 40, 60, 60, 60, 60, 60, 60, 60, 60, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 40, 60, 60, 60, 60, 4, 1, 1, 1, 1, 1, 4, 4, 4] 60
rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 138
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042383 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NC=C(C2=CC=CC=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 23, 59, 59, 59, 59, 59, 60, 60, 59, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 7, 7, 7, 23, 59, 59, 59, 59, 1, 4, 4, 1, 4, 4, 2, 2, 2] 60
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 131
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042383 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042383
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042383/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042383/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042383
Building REAL300000042384
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042384'
/scratch/stefan/7769623/working/building/REAL300000042384 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042384

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042384/0 /scratch/stefan/7769623/working/building/REAL300000042384 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/422
`/scratch/stefan/7769623/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(Cl)C=C3)CC2)=C1)

`REAL300000042384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042384 none O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(Cl)C=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 26, 26, 23, 23, 26, 26, 23, 23, 1, 1, 1, 1, 23, 23, 23, 23, 26, 26, 26, 26, 23, 23, 23, 23, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042384 none O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(Cl)C=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 20, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 26] 26
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 37
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042384 none O=C([O-])C1=CC=CC(N=NC2CC=C(C3=CC=C(Cl)C=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 12, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 1, 1, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 23] 26
rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 21, 22, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 31, 32, 33, 34, 39])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042384 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042384
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042384/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042384
Building REAL300000042385
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042385'
/scratch/stefan/7769623/working/building/REAL300000042385 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042385

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042385/0 /scratch/stefan/7769623/working/building/REAL300000042385 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/423
`/scratch/stefan/7769623/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1CCCCN1C(=O)OC(C)(C)C)

`REAL300000042385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042385 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 65, 65, 65, 65, 65, 65, 65, 75, 75, 94, 94, 94, 94, 40, 40, 40, 40, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 94, 94, 94, 94, 94, 94, 94, 94, 94] 94
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 294
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042385 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 27, 27, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 16, 16, 5, 5, 5, 5, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 94
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 128
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042385 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042385
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042385/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042385
Building REAL300000042386
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042386'
/scratch/stefan/7769623/working/building/REAL300000042386 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042386

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042386/0 /scratch/stefan/7769623/working/building/REAL300000042386 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/424
`/scratch/stefan/7769623/working/3D/424' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCCN1C(=O)OC(C)(C)C)

`REAL300000042386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042386 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [38, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 58, 58, 58, 58, 58, 58, 58, 75, 75, 99, 99, 99, 99, 38, 38, 38, 38, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 99, 99, 99, 99, 99, 99, 99, 99, 99] 99
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 311
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042386 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 25, 25, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 19, 19, 19, 5, 5, 5, 5, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 99
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 130
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042386 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042386
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042386/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042386
Building REAL300000042387
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042387'
/scratch/stefan/7769623/working/building/REAL300000042387 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042387

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042387/0 /scratch/stefan/7769623/working/building/REAL300000042387 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/425
`/scratch/stefan/7769623/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(O)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1[N+](=O)[O-])

`REAL300000042387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042387 none COC1=C(O)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 2, 2, 4, 4, 4, 2, 1, 1, 7, 28, 60, 60, 60, 60] 120
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 117
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042387 none COC1=C(O)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 60, 60, 60, 60, 60, 60, 60, 120, 60, 60, 33, 9, 1, 1, 1, 1] 120
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 222
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042387 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042387
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042387/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042387
Building REAL300000042388
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042388'
/scratch/stefan/7769623/working/building/REAL300000042388 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042388

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042388/0 /scratch/stefan/7769623/working/building/REAL300000042388 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/426
`/scratch/stefan/7769623/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042388 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [10, 9, 10, 10, 5, 3, 5, 1, 1, 1, 1, 1, 1, 6, 6, 34, 64, 64, 64, 64, 65, 65, 65, 64, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 1, 1, 6, 34, 64, 64, 64, 64, 1, 1] 158
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 45, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042388 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 158, 158, 158, 144, 100, 144, 65, 53, 65, 64, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 65, 65, 158, 158, 158, 158, 158, 158, 158, 158, 158, 100, 65, 64, 34, 8, 1, 1, 1, 1, 65, 65] 158
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 495
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042388 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042388
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042388/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042388
Building REAL300000042389
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042389'
/scratch/stefan/7769623/working/building/REAL300000042389 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042389

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042389/0 /scratch/stefan/7769623/working/building/REAL300000042389 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/427
`/scratch/stefan/7769623/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCN1C(=O)OC(C)(C)C)

`REAL300000042389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042389 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 7, 34, 34, 33, 34, 34, 34, 34, 34, 1, 1, 1, 1, 6, 6, 20, 24, 25, 24, 2, 2, 2, 1, 1, 34, 34, 33, 34, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 100
rigid atoms, others: [0, 1, 2, 3, 36, 33, 34, 14, 15, 16, 17, 35, 27, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 117
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042389 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 64, 64, 96, 100, 100, 100, 34, 34, 34, 34, 34, 1, 1, 1, 1, 34, 34, 34, 34, 100, 100, 100, 100, 100, 100, 100, 100, 100] 100
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042389 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042389
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042389/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042389
Building REAL300000042390
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042390'
/scratch/stefan/7769623/working/building/REAL300000042390 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042390

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042390/0 /scratch/stefan/7769623/working/building/REAL300000042390 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/428
`/scratch/stefan/7769623/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCNC(=O)OC(C)(C)C)CC(C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042390 none CC(CCNC(=O)OC(C)(C)C)CC(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 34, 57, 60, 142, 182, 182, 201, 201, 201, 201, 17, 5, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 34, 57, 57, 60, 60, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 17, 17, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [51, 50, 16, 17, 18, 19, 20, 21, 22, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 722
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042390 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042390
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042390/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042390
Building REAL300000042391
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042391'
/scratch/stefan/7769623/working/building/REAL300000042391 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042391

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042391/0 /scratch/stefan/7769623/working/building/REAL300000042391 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/429
`/scratch/stefan/7769623/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CC(C2=NOC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2)C1)

`REAL300000042391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042391 none CC(C)(C)OC(=O)N1CC(C2=NOC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2)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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 8, 10, 10, 2, 1, 2, 1, 1, 1, 1, 13, 13, 13, 13, 26, 26, 76, 120, 120, 120, 120, 120, 120, 120, 120, 13, 1, 11, 11, 11, 10, 10, 10, 11, 11, 11, 1, 1, 1, 26, 76, 120, 120, 120, 120, 13, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 39, 47, 48, 27, 5] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 288
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042391 none CC(C)(C)OC(=O)N1CC(C2=NOC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2)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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 167, 120, 167, 120, 120, 35, 35, 35, 36, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 120, 28, 6, 1, 1, 1, 1, 36, 120, 120] 201
rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48])
total number of confs: 534
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042391 none CC(C)(C)OC(=O)N1CC(C2=NOC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2)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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 68, 68, 24, 13, 24, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 19, 36, 36, 36, 36, 36, 36, 36, 36, 1, 13, 68, 68, 68, 68, 68, 68, 68, 68, 68, 13, 13, 13, 4, 18, 36, 36, 36, 35, 1, 13, 13] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48])
total number of confs: 240
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042391 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042391/1 /scratch/stefan/7769623/working/building/REAL300000042391 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/430
`/scratch/stefan/7769623/working/3D/430' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CC(C2=NOC(CN=NC3=CC=CC(C(=O)[O-])=C3)=C2)C1)

`REAL300000042391.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042391/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042391 none CC(C)(C)OC(=O)N1CC(C2=NOC(CN=NC3=CC=CC(C(=O)[O-])=C3)=C2)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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 11, 11, 11, 11, 39, 134, 134, 158, 158, 158, 158, 158, 158, 158, 158, 11, 1, 5, 5, 5, 4, 4, 4, 5, 5, 5, 1, 1, 1, 39, 39, 158, 158, 158, 158, 11, 1, 1] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 39, 47, 48, 27, 5] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 316
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042391 none CC(C)(C)OC(=O)N1CC(C2=NOC(CN=NC3=CC=CC(C(=O)[O-])=C3)=C2)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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 200, 158, 200, 158, 158, 51, 51, 51, 51, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 20, 20, 1, 1, 1, 1, 51, 158, 158] 201
rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48])
total number of confs: 573
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042391 none CC(C)(C)OC(=O)N1CC(C2=NOC(CN=NC3=CC=CC(C(=O)[O-])=C3)=C2)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.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 12, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 21, 21, 19, 11, 19, 11, 11, 1, 1, 1, 1, 1, 1, 5, 32, 32, 51, 51, 51, 51, 51, 51, 51, 51, 1, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 5, 5, 51, 51, 51, 51, 1, 11, 11] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042391 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042391
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042391/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042391/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042391
Building REAL300000042392
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042392'
/scratch/stefan/7769623/working/building/REAL300000042392 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042392

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042392/0 /scratch/stefan/7769623/working/building/REAL300000042392 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/431
`/scratch/stefan/7769623/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(F)C=C32)=CC=C1)

`REAL300000042392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042392 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(F)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 1, 1, 1, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [2, 1, 2, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 40, 20, 1, 1, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042392 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(F)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 1, 1, 1, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [21, 20, 21, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 2, 1, 20, 20, 20] 42
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 28] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 27, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042392 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042392/1 /scratch/stefan/7769623/working/building/REAL300000042392 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/432
`/scratch/stefan/7769623/working/3D/432' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(F)C=C32)=CC=C1)

`REAL300000042392.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042392/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042392 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(F)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 7, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042392 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(F)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 15, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 9, 9, 9] 9
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042392 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042392
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042392/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042392/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042392
Building REAL300000042393
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042393'
/scratch/stefan/7769623/working/building/REAL300000042393 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042393

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042393/0 /scratch/stefan/7769623/working/building/REAL300000042393 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/433
`/scratch/stefan/7769623/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NC3=C(Br)C=CC=C23)=C1)

`REAL300000042393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042393 none O=C([O-])C1=CC=CC(NN=CC2=CC=NC3=C(Br)C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 13, 41, 41, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 13, 41, 70, 70, 70, 70, 70, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042393 none O=C([O-])C1=CC=CC(NN=CC2=CC=NC3=C(Br)C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 70, 70, 70, 70, 51, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 51, 12, 1, 1, 1, 1, 1, 70] 70
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042393 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042393
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042393/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042393
Building REAL300000042394
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042394'
/scratch/stefan/7769623/working/building/REAL300000042394 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042394

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042394/0 /scratch/stefan/7769623/working/building/REAL300000042394 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/434
`/scratch/stefan/7769623/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=C1)

`REAL300000042394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042394 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 32, 32, 32, 32, 69, 69, 87, 201, 201, 201, 201, 201, 201, 32, 1, 1, 1, 1, 8, 31, 32, 32, 201, 201, 201, 201, 201, 201, 201, 32, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 690
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042394 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 165, 73, 73, 71, 72, 72, 72, 31, 20, 31, 4, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 165, 73, 72, 72, 4, 4, 1, 1, 1, 1, 1, 72, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 479
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042394 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)OCC3=CC=CC=C3)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 10, 40, 72, 72, 41, 72, 71, 1, 32, 32, 32, 32, 12, 3, 1, 1, 40, 40, 72, 72, 41, 72, 72, 1, 32] 201
rigid atoms, others: [32, 33, 41, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 324
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042394 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042394
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042394/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042394
Building REAL300000042395
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042395'
/scratch/stefan/7769623/working/building/REAL300000042395 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042395

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042395/0 /scratch/stefan/7769623/working/building/REAL300000042395 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/435
`/scratch/stefan/7769623/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=C1)

`REAL300000042395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042395 none O=C([O-])C1=CC=CC(NN=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 46, 46, 46, 46, 74, 74, 87, 201, 201, 201, 201, 201, 201, 46, 1, 1, 1, 1, 5, 23, 46, 46, 201, 201, 201, 201, 201, 201, 201, 46, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 674
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042395 none O=C([O-])C1=CC=CC(NN=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 186, 113, 113, 62, 62, 62, 62, 35, 20, 35, 4, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 186, 113, 62, 62, 4, 4, 1, 1, 1, 1, 1, 62, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 546
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042395 none O=C([O-])C1=CC=CC(NN=CC2=CNC(C(=O)OCC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 25, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 10, 33, 62, 62, 34, 62, 61, 1, 46, 46, 46, 46, 25, 7, 1, 1, 33, 33, 62, 62, 34, 62, 62, 1, 46] 201
rigid atoms, others: [32, 33, 41, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042395 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042395
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042395/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042395
Building REAL300000042396
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042396'
/scratch/stefan/7769623/working/building/REAL300000042396 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042396

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042396/0 /scratch/stefan/7769623/working/building/REAL300000042396 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/436
`/scratch/stefan/7769623/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(I)C=C2)=C1)

`REAL300000042396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042396 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(I)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 18, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 34, 34, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 10, 34, 35, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042396 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(I)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 18, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 28, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 28, 4, 1, 1, 1, 1, 35] 35
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042396 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042396
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042396/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042396
Building REAL300000042397
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042397'
/scratch/stefan/7769623/working/building/REAL300000042397 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042397

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042397/0 /scratch/stefan/7769623/working/building/REAL300000042397 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/437
`/scratch/stefan/7769623/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CN1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1)

`REAL300000042397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042397 none COC(=O)CN1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 8, 41, 1, 1, 1, 1, 1, 6, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 41, 41, 41, 8, 8, 1, 6, 6, 49, 49, 49, 49] 201
rigid atoms, others: [4, 5, 6, 7, 8, 20, 21, 27] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042397 none COC(=O)CN1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 131, 201, 49, 49, 49, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 201, 201, 201, 131, 131, 49, 25, 25, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 689
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042397 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042397/1 /scratch/stefan/7769623/working/building/REAL300000042397 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/438
`/scratch/stefan/7769623/working/3D/438' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1)

`REAL300000042397.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042397/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042397 none COC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 8, 74, 1, 1, 1, 1, 1, 4, 4, 18, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 74, 74, 74, 8, 8, 1, 4, 18, 39, 39, 39, 39] 201
rigid atoms, others: [4, 5, 6, 7, 8, 20, 21, 27] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042397 none COC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 129, 201, 39, 39, 39, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 201, 201, 201, 129, 129, 39, 30, 6, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 672
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042397 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042397
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042397/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042397/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042397
Building REAL300000042398
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042398'
/scratch/stefan/7769623/working/building/REAL300000042398 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042398

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042398/0 /scratch/stefan/7769623/working/building/REAL300000042398 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/439
`/scratch/stefan/7769623/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C2C=CC(F)=C3Br)=C1)

`REAL300000042398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042398 none O=C([O-])C1=CC=CC(NN=C2CCC3=C2C=CC(F)=C3Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 26
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042398 none O=C([O-])C1=CC=CC(NN=C2CCC3=C2C=CC(F)=C3Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 25
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042398 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042398
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042398/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042398
Building REAL300000042399
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042399'
/scratch/stefan/7769623/working/building/REAL300000042399 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042399

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042399/0 /scratch/stefan/7769623/working/building/REAL300000042399 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/440
`/scratch/stefan/7769623/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC1=CC=CS1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042399 none CN(CC1=CC=CS1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 1, 1, 1, 1, 1, 1, 19, 25, 25, 25, 25, 96, 96, 164, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 19, 19, 19, 5, 5, 1, 1, 1, 25, 25, 96, 164, 201, 201, 201, 201, 25, 25] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 506
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042399 none CN(CC1=CC=CS1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 67, 137, 201, 201, 201, 201, 38, 38, 38, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 67, 67, 67, 137, 137, 201, 201, 201, 38, 38, 18, 4, 1, 1, 1, 1, 38, 38] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 635
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042399 none CN(CC1=CC=CS1)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 13, 25, 25, 25, 25, 1, 1, 1, 1, 1, 6, 6, 22, 38, 38, 38, 38, 38, 39, 39, 38, 1, 1, 3, 3, 3, 13, 13, 25, 25, 25, 1, 1, 6, 22, 38, 38, 38, 38, 1, 1] 201
rigid atoms, others: [1, 34, 35, 8, 9, 10, 11, 12, 43, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 145
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042399 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042399
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042399/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042399
Building REAL300000042400
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042400'
/scratch/stefan/7769623/working/building/REAL300000042400 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042400

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042400/0 /scratch/stefan/7769623/working/building/REAL300000042400 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/441
`/scratch/stefan/7769623/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CC=C21)

`REAL300000042400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042400 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 10, 10, 57, 134, 134, 134, 134, 134, 135, 135, 134, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 10, 57, 134, 134, 134, 134, 1, 1, 1, 1, 1] 135
rigid atoms, others: [1, 2, 3, 4, 5, 35, 38, 34, 17, 18, 19, 20, 21, 22, 23, 36, 27, 37] set([0, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 258
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042400 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [134, 134, 134, 134, 58, 58, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 134, 134, 134, 134, 134, 134, 134, 135, 135, 135, 134, 58, 12, 1, 1, 1, 1, 134, 134, 134, 134, 134] 135
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 208
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042400 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042400
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042400/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042400
Building REAL300000042401
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042401'
/scratch/stefan/7769623/working/building/REAL300000042401 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042401

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042401/0 /scratch/stefan/7769623/working/building/REAL300000042401 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/442
`/scratch/stefan/7769623/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC1=CN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042401 none CSCC1=CN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 7, 43, 44, 77, 77, 77, 77, 77, 77, 77, 77, 1, 21, 21, 21, 7, 7, 1, 7, 7, 77, 77, 77, 77] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042401 none CSCC1=CN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 76, 76, 76, 76, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 76, 201, 201, 201, 148, 148, 76, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 598
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042401 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042401/1 /scratch/stefan/7769623/working/building/REAL300000042401 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/443
`/scratch/stefan/7769623/working/3D/443' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042401.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042401/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042401 none CSCC1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 7, 7, 31, 68, 68, 68, 68, 68, 68, 68, 68, 1, 34, 34, 34, 9, 9, 1, 7, 31, 68, 68, 68, 68] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042401 none CSCC1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 68, 68, 68, 68, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 201, 201, 201, 137, 137, 68, 40, 8, 1, 1, 1, 1] 201
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 553
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042401 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042401
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042401/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042401/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042401
Building REAL300000042402
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042402'
/scratch/stefan/7769623/working/building/REAL300000042402 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042402

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042402/0 /scratch/stefan/7769623/working/building/REAL300000042402 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/444
`/scratch/stefan/7769623/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC=C(Br)C=C32)=C1)

`REAL300000042402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042402 none O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042402 none O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 38])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042402 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042402
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042402/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042402
Building REAL300000042403
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042403'
/scratch/stefan/7769623/working/building/REAL300000042403 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042403

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042403/0 /scratch/stefan/7769623/working/building/REAL300000042403 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/445
`/scratch/stefan/7769623/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1)

`REAL300000042403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042403 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 109, 109, 109, 109, 201, 201, 177, 201, 201, 201, 109, 49, 49, 49, 10, 1, 1, 1, 1, 109, 201, 201, 200, 201] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37])
total number of confs: 427
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: REAL300000042403 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 52, 52, 148, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 53, 53, 53, 148, 201, 201, 201, 201, 12, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 475
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042403 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 110, 110, 110, 110, 110, 110, 110, 109, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 13, 1, 12, 12, 12, 37, 110, 110, 110, 109, 1, 12, 12, 12, 12] 201
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 229
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042403 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042403/1 /scratch/stefan/7769623/working/building/REAL300000042403 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/446
`/scratch/stefan/7769623/working/3D/446' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1)

`REAL300000042403.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042403/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042403 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 88, 88, 88, 88, 201, 201, 117, 201, 201, 201, 88, 22, 22, 22, 22, 1, 1, 1, 1, 88, 201, 201, 201, 201] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37])
total number of confs: 646
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042403 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 71, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 71, 71, 71, 71, 201, 201, 201, 201, 12, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 436
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042403 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 15, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 43, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 13, 1, 9, 9, 9, 9, 88, 88, 88, 88, 1, 13, 13, 10, 13] 201
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 189
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042403 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042403
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042403/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042403/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042403
Building REAL300000042404
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042404'
/scratch/stefan/7769623/working/building/REAL300000042404 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042404

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042404/0 /scratch/stefan/7769623/working/building/REAL300000042404 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/447
`/scratch/stefan/7769623/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(O)C3=CC=CC=C3C=C2)=C1)

`REAL300000042404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042404 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 10, 30, 68, 34, 34, 34, 34, 34, 34, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 124
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042404 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C3=CC=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 26, 6, 2, 1, 1, 1, 1, 1, 1, 34] 68
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 76
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042404 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042404
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042404/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042404
Building REAL300000042405
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042405'
/scratch/stefan/7769623/working/building/REAL300000042405 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042405

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042405/0 /scratch/stefan/7769623/working/building/REAL300000042405 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/448
`/scratch/stefan/7769623/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC=C3Cl)C2)=C1)

`REAL300000042405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042405 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC=C3Cl)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 1, 1, 1, 1, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 107
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: REAL300000042405 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC=C3Cl)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 50] 50
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 72
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042405 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=CC=C3Cl)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 35, 35, 35, 35, 1, 1, 1, 1, 6, 6, 2, 6, 1, 1, 35] 50
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 32, 35])
total number of confs: 58
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042405 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042405
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042405/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042405
Building REAL300000042406
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042406'
/scratch/stefan/7769623/working/building/REAL300000042406 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042406

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042406/0 /scratch/stefan/7769623/working/building/REAL300000042406 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/449
`/scratch/stefan/7769623/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3CCCC3)C=C2)=C1)

`REAL300000042406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042406 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3CCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 43, 43, 52, 52, 43, 43, 133, 133, 133, 133, 52, 52, 1, 1, 1, 1, 13, 43, 52, 52, 133, 133, 133, 133, 133, 133, 133, 133, 133, 52, 52, 1] 133
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 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: REAL300000042406 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3CCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 133, 133, 133, 133, 133, 85, 17, 17, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 133, 133, 133, 133, 85, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 133] 133
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41])
total number of confs: 297
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042406 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3CCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 52, 52, 52, 52, 29, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 52, 52, 52, 52, 29, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 52] 133
rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41])
total number of confs: 118
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042406 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042406
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042406/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042406
Building REAL300000042407
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042407'
/scratch/stefan/7769623/working/building/REAL300000042407 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042407

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042407/0 /scratch/stefan/7769623/working/building/REAL300000042407 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/450
`/scratch/stefan/7769623/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)O2)=C1)

`REAL300000042407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042407 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 42, 42, 42, 42, 42, 1, 1, 1, 1, 13, 33, 42, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042407 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 42, 41, 42, 42, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 42, 41, 42, 42, 28, 6, 1, 1, 42] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042407 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042407
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042407/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042407
Building REAL300000042408
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042408'
/scratch/stefan/7769623/working/building/REAL300000042408 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042408

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042408/0 /scratch/stefan/7769623/working/building/REAL300000042408 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/451
`/scratch/stefan/7769623/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(OC(F)F)C2=CC=CC=C2C=C1)

`REAL300000042408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042408 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(OC(F)F)C2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 4, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 36
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042408 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(OC(F)F)C2=CC=CC=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 13, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1] 19
rigid atoms, others: [1, 36, 37, 38, 39, 40, 41, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 72
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042408 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042408
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042408/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042408
Building REAL300000042409
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042409'
/scratch/stefan/7769623/working/building/REAL300000042409 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042409

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042409/0 /scratch/stefan/7769623/working/building/REAL300000042409 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/452
`/scratch/stefan/7769623/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(C=C1[N+](=O)[O-])OCO2)

`REAL300000042409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042409 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(C=C1[N+](=O)[O-])OCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 3, 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: [32, 32, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 32, 32, 12, 1, 1, 1, 1, 41, 41, 41, 41] 41
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042409 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(C=C1[N+](=O)[O-])OCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 17, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 17, 41, 41, 41, 41, 1, 1, 1, 1] 41
rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042409 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042409
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042409/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042409
Building REAL300000042410
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042410'
/scratch/stefan/7769623/working/building/REAL300000042410 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042410

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042410/0 /scratch/stefan/7769623/working/building/REAL300000042410 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/453
`/scratch/stefan/7769623/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C=C1F)

`REAL300000042410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042410 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [77, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 105, 105, 58, 105, 105, 105, 105, 77, 77, 77, 77, 77, 8, 1, 1, 1, 1, 105, 105, 105] 116
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 524
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042410 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [31, 12, 1, 12, 12, 64, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 64, 105, 105, 105, 105, 1, 1, 1] 116
rigid atoms, others: [32, 33, 2, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 312
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042410 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042410
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042410/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042410
Building REAL300000042411
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042411'
/scratch/stefan/7769623/working/building/REAL300000042411 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042411

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042411/0 /scratch/stefan/7769623/working/building/REAL300000042411 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/454
`/scratch/stefan/7769623/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC(Br)=CC=C32)=C1)

`REAL300000042411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042411 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(Br)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 26
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042411 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(Br)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24])
total number of confs: 25
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042411 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042411
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042411/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042411
Building REAL300000042412
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042412'
/scratch/stefan/7769623/working/building/REAL300000042412 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042412

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042412/0 /scratch/stefan/7769623/working/building/REAL300000042412 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/455
`/scratch/stefan/7769623/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC)C=C1)

`REAL300000042412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042412 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [107, 97, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 137, 137, 38, 49, 168, 137, 137, 107, 107, 107, 107, 107, 97, 97, 8, 1, 1, 1, 1, 137, 137, 168, 168, 168, 137, 137] 196
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 14, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 839
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042412 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [37, 26, 7, 1, 7, 7, 42, 137, 137, 137, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 2, 1, 1, 37, 37, 37, 37, 37, 26, 26, 42, 137, 137, 137, 137, 1, 1, 3, 3, 3, 1, 1] 196
rigid atoms, others: [19, 3, 36, 40, 41, 15, 16, 17, 18, 35, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 378
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042412 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042412
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042412/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042412
Building REAL300000042413
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042413'
/scratch/stefan/7769623/working/building/REAL300000042413 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042413

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042413/0 /scratch/stefan/7769623/working/building/REAL300000042413 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/456
`/scratch/stefan/7769623/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3)C2)=C1)

`REAL300000042413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042413 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 35, 35, 35, 45, 45, 35, 35, 45, 45, 35, 1, 1, 1, 1, 35, 35, 35, 35, 45, 45, 45, 45, 35, 35, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 119
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: REAL300000042413 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 27, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 45, 45, 45, 45, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 45] 45
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 70
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042413 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 12, 12, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 35, 35, 35, 35, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 35] 45
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 20, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31, 32, 35])
total number of confs: 55
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042413 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042413
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042413/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042413
Building REAL300000042414
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042414'
/scratch/stefan/7769623/working/building/REAL300000042414 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042414

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042414/0 /scratch/stefan/7769623/working/building/REAL300000042414 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/457
`/scratch/stefan/7769623/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCC1)

`REAL300000042414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042414 none CC(C)(C)OC(=O)NCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCC1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 41, 42, 42, 32, 21, 32, 7, 1, 1, 1, 7, 41, 41, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 21, 7, 7, 7, 7, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 47, 48, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042414 none CC(C)(C)OC(=O)NCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCC1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 194, 167, 194, 114, 80, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 114, 114, 24, 24, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80] 201
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48])
total number of confs: 697
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042414 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042414
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042414/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042414
Building REAL300000042415
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042415'
/scratch/stefan/7769623/working/building/REAL300000042415 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042415

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042415/0 /scratch/stefan/7769623/working/building/REAL300000042415 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/458
`/scratch/stefan/7769623/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCOC3=CC(F)=CC(F)=C32)=C1)

`REAL300000042415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042415 none O=C([O-])C1=CC=CC(NN=C2CCCOC3=CC(F)=CC(F)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 1, 1, 1, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([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: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042415 none O=C([O-])C1=CC=CC(NN=C2CCCOC3=CC(F)=CC(F)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 24, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 24, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 27, 36])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042415 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042415
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042415/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042415
Building REAL300000042416
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042416'
/scratch/stefan/7769623/working/building/REAL300000042416 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042416

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042416/0 /scratch/stefan/7769623/working/building/REAL300000042416 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/459
`/scratch/stefan/7769623/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CN2)=C1)

`REAL300000042416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042416 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CN2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 31, 31, 36, 36, 36, 36, 36, 1, 1, 1, 1, 13, 31, 36, 36, 36, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042416 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CN2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 35, 36, 36, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 36, 35, 36, 36, 24, 6, 1, 1, 1, 36] 36
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 26])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042416 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042416
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042416/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042416
Building REAL300000042417
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042417'
/scratch/stefan/7769623/working/building/REAL300000042417 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042417

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042417/0 /scratch/stefan/7769623/working/building/REAL300000042417 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/460
`/scratch/stefan/7769623/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(C)(CN=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1)

`REAL300000042417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042417 none C[NH+](C)CC(C)(CN=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 12, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 11, 11, 1, 1, 1, 1, 13, 13, 13, 13, 13] 13
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46])
total number of confs: 51
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042417 none C[NH+](C)CC(C)(CN=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 1, 5, 5, 7, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 13, 13, 13, 13, 1, 1, 1, 1, 1] 13
rigid atoms, others: [5, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 38
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042417 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042417
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042417/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042417
Building REAL300000042418
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042418'
/scratch/stefan/7769623/working/building/REAL300000042418 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042418

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042418/0 /scratch/stefan/7769623/working/building/REAL300000042418 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/461
`/scratch/stefan/7769623/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1F)

`REAL300000042418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042418 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 41, 41, 41, 42, 42, 41, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 7, 41, 41, 41, 41, 1] 42
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 18, 19, 20, 21, 22, 23, 27, 28] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 29, 30, 31])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042418 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 41, 41, 41, 41, 41, 41, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 41, 42, 42, 42, 41, 41, 12, 1, 1, 1, 1, 41] 42
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 70
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042418 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042418
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042418/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042418
Building REAL300000042419
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042419'
/scratch/stefan/7769623/working/building/REAL300000042419 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042419

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042419/0 /scratch/stefan/7769623/working/building/REAL300000042419 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/462
`/scratch/stefan/7769623/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)F)

`REAL300000042419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042419 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 125, 125, 78, 125, 125, 125, 164, 189, 189, 56, 56, 56, 56, 56, 6, 1, 1, 1, 1, 125, 125, 125, 125, 189] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 700
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042419 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 9, 1, 9, 9, 47, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 20, 20, 20, 20, 20, 47, 125, 125, 125, 125, 1, 1, 1, 1, 27] 201
rigid atoms, others: [2, 35, 36, 37, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 361
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042419 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042419
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042419/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042419
Building REAL300000042420
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042420'
/scratch/stefan/7769623/working/building/REAL300000042420 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042420

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042420/0 /scratch/stefan/7769623/working/building/REAL300000042420 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/463
`/scratch/stefan/7769623/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2=NC=CN2C)C=C1)

`REAL300000042420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042420 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2=NC=CN2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 91, 91, 32, 62, 137, 151, 201, 201, 201, 201, 201, 91, 91, 33, 33, 33, 8, 1, 1, 1, 1, 91, 91, 151, 151, 201, 201, 201, 201, 201, 91, 91] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 600
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: REAL300000042420 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2=NC=CN2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 26, 69, 69, 159, 201, 201, 201, 201, 201, 201, 201, 201, 26, 26, 26, 16, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 69, 69, 69, 159, 201, 201, 201, 201, 26, 26, 8, 8, 1, 1, 2, 2, 2, 26, 26] 201
rigid atoms, others: [39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45])
total number of confs: 511
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042420 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCC2=NC=CN2C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 1, 1, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 31, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 2, 10, 26, 26, 26, 26, 26, 1, 1, 6, 6, 6, 31, 91, 91, 91, 91, 1, 1, 10, 10, 26, 26, 27, 27, 27, 1, 1] 201
rigid atoms, others: [1, 45, 35, 36, 44, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 217
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042420 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042420
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042420/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042420
Building REAL300000042421
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042421'
/scratch/stefan/7769623/working/building/REAL300000042421 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042421

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042421/0 /scratch/stefan/7769623/working/building/REAL300000042421 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/464
`/scratch/stefan/7769623/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(F)C=C1)

`REAL300000042421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042421 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 9, 9, 59, 59, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 2, 2, 2, 9, 9, 9, 9, 155, 155, 155, 155, 6, 6, 6, 6] 170
rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 244
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042421 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 28, 28, 123, 123, 170, 170, 170, 170, 170, 170, 170, 170, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 170, 170, 170, 170, 1, 1, 1, 1] 170
rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 289
number of broken/clashed sets: 58
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042421 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 15, 1, 1, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [155, 155, 62, 8, 62, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 155, 155, 155, 155, 170, 170, 155, 170, 170, 170, 155, 155, 155, 62, 62, 62, 62, 1, 1, 1, 1, 170, 170, 170, 170] 170
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 435
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042421 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042421
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042421/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042421
Building REAL300000042422
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042422'
/scratch/stefan/7769623/working/building/REAL300000042422 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042422

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042422/0 /scratch/stefan/7769623/working/building/REAL300000042422 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/465
`/scratch/stefan/7769623/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(C)C=C1)

`REAL300000042422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042422 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 58, 58, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 2, 2, 2, 9, 9, 9, 9, 152, 152, 152, 152, 6, 6, 6, 6, 6, 6, 6] 169
rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 258
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042422 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 26, 26, 122, 122, 169, 169, 169, 169, 169, 169, 169, 169, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 169, 169, 169, 169, 1, 1, 2, 2, 2, 1, 1] 169
rigid atoms, others: [37, 38, 42, 43, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41])
total number of confs: 289
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042422 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=C(C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [152, 152, 59, 8, 59, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 152, 152, 152, 152, 169, 169, 152, 169, 169, 169, 152, 152, 152, 59, 59, 59, 59, 1, 1, 1, 1, 169, 169, 169, 169, 169, 169, 169] 169
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 438
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042422 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042422
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042422/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042422
Building REAL300000042423
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042423'
/scratch/stefan/7769623/working/building/REAL300000042423 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042423

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042423/0 /scratch/stefan/7769623/working/building/REAL300000042423 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/466
`/scratch/stefan/7769623/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=CC(Cl)=C1)

`REAL300000042423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042423 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 39, 39, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 11, 11, 3, 11, 11, 11, 2, 2, 2, 8, 8, 8, 8, 88, 88, 88, 88, 11, 11, 9, 11] 201
rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 175
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: REAL300000042423 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 42, 42, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 42, 42, 42, 42, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 372
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042423 none CC1=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)N=NN1C1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 42, 8, 42, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 88, 88, 88, 88, 201, 201, 201, 201, 201, 201, 88, 88, 88, 42, 42, 42, 42, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 373
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042423 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042423
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042423/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042423
Building REAL300000042424
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042424'
/scratch/stefan/7769623/working/building/REAL300000042424 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042424

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042424/0 /scratch/stefan/7769623/working/building/REAL300000042424 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/467
`/scratch/stefan/7769623/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1)

`REAL300000042424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042424 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 44, 44, 16, 18, 148, 163, 163, 148, 163, 163, 44, 44, 32, 32, 32, 32, 32, 30, 30, 3, 1, 1, 1, 1, 44, 44, 163, 163, 148, 163, 163, 44, 44] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 14, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 436
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042424 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 86, 55, 8, 55, 55, 146, 163, 163, 163, 163, 163, 163, 163, 163, 8, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 89, 89, 89, 89, 89, 86, 86, 146, 163, 163, 163, 163, 18, 18, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48])
total number of confs: 621
number of broken/clashed sets: 78
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042424 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 12, 6, 1, 6, 6, 29, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 9, 18, 18, 9, 18, 18, 1, 1, 14, 14, 14, 14, 14, 12, 12, 29, 44, 44, 44, 44, 1, 1, 18, 18, 9, 18, 18, 1, 1] 201
rigid atoms, others: [48, 3, 40, 41, 47, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 178
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042424 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042424
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042424/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042424
Building REAL300000042425
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042425'
/scratch/stefan/7769623/working/building/REAL300000042425 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042425

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042425/0 /scratch/stefan/7769623/working/building/REAL300000042425 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/468
`/scratch/stefan/7769623/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(C)=CNC2=O)C=C1)

`REAL300000042425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042425 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(C)=CNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 103, 103, 74, 94, 167, 168, 168, 168, 168, 168, 103, 103, 54, 54, 54, 10, 1, 1, 1, 1, 103, 103, 168, 168, 168, 168, 168, 103, 103] 168
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 413
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: REAL300000042425 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(C)=CNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [26, 5, 26, 26, 99, 168, 168, 168, 168, 168, 168, 168, 168, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 26, 26, 99, 168, 168, 168, 168, 9, 9, 2, 2, 2, 1, 1, 9, 9] 168
rigid atoms, others: [39, 40, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42])
total number of confs: 377
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042425 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(C)=CNC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 5, 1, 8, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [6, 1, 6, 6, 33, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 6, 6, 6, 33, 103, 103, 103, 103, 1, 1, 9, 9, 9, 9, 9, 1, 1] 168
rigid atoms, others: [1, 34, 35, 41, 42, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 182
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042425 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042425
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042425/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042425
Building REAL300000042426
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042426'
/scratch/stefan/7769623/working/building/REAL300000042426 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042426

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042426/0 /scratch/stefan/7769623/working/building/REAL300000042426 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/469
`/scratch/stefan/7769623/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OCCCC(=O)[O-])=C1)

`REAL300000042426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042426 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 25, 25, 25, 25, 25, 70, 113, 149, 201, 201, 201, 25, 8, 8, 8, 3, 1, 1, 1, 1, 25, 25, 25, 113, 113, 149, 149, 201, 201, 25] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 786
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042426 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 21, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 7, 18, 34, 66, 93, 93, 1, 9, 9, 9, 21, 25, 25, 25, 25, 1, 1, 1, 18, 18, 34, 34, 66, 66, 1] 201
rigid atoms, others: [1, 34, 35, 36, 43, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 462
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042426 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042426
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042426/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042426
Building REAL300000042427
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042427'
/scratch/stefan/7769623/working/building/REAL300000042427 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042427

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042427/0 /scratch/stefan/7769623/working/building/REAL300000042427 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/470
`/scratch/stefan/7769623/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042427 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 4, 1, 1, 1, 1, 1, 1, 11, 29, 29, 40, 40, 1, 1, 13, 46, 46, 78, 78, 78, 78, 78, 78, 78, 78, 13, 13, 13, 13, 5, 5, 4, 4, 1, 1, 29, 29, 29, 29, 1, 1, 78, 78, 78, 78] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 273
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042427 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 7, 31, 66, 71, 78, 78, 71, 78, 171, 201, 201, 201, 201, 78, 78, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 70, 70, 71, 71, 78, 78, 201, 201, 201, 201, 78, 78, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 653
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042427 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042427
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042427/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042427
Building REAL300000042428
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042428'
/scratch/stefan/7769623/working/building/REAL300000042428 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042428

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042428/0 /scratch/stefan/7769623/working/building/REAL300000042428 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/471
`/scratch/stefan/7769623/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042428 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 4, 1, 1, 1, 1, 1, 1, 6, 22, 37, 37, 1, 1, 13, 51, 51, 79, 79, 79, 79, 79, 79, 79, 79, 13, 13, 13, 13, 5, 5, 4, 4, 1, 1, 22, 22, 1, 1, 79, 79, 79, 79] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43])
total number of confs: 261
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042428 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 7, 27, 66, 70, 79, 79, 70, 79, 176, 201, 201, 201, 79, 79, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 27, 27, 69, 69, 70, 70, 79, 79, 201, 201, 79, 79, 1, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 623
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042428 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042428
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042428/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042428
Building REAL300000042429
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042429'
/scratch/stefan/7769623/working/building/REAL300000042429 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042429

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042429/0 /scratch/stefan/7769623/working/building/REAL300000042429 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/472
`/scratch/stefan/7769623/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1)

`REAL300000042429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042429 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 65, 65, 65, 65, 65, 174, 201, 201, 201, 201, 65, 17, 17, 17, 3, 1, 1, 1, 1, 65, 65, 65, 201, 201, 201, 201, 65] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 403
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042429 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 35, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 11, 27, 27, 40, 40, 1, 10, 10, 10, 35, 65, 65, 65, 65, 1, 1, 1, 27, 27, 27, 27, 1] 201
rigid atoms, others: [1, 34, 35, 33, 40, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 265
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042429 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042429
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042429/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042429
Building REAL300000042430
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042430'
/scratch/stefan/7769623/working/building/REAL300000042430 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042430

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042430/0 /scratch/stefan/7769623/working/building/REAL300000042430 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/473
`/scratch/stefan/7769623/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042430 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 4, 3, 1, 1, 1, 1, 1, 1, 6, 16, 17, 25, 22, 1, 1, 11, 42, 42, 74, 74, 74, 74, 74, 74, 74, 74, 11, 11, 11, 11, 4, 4, 3, 3, 1, 1, 16, 16, 17, 17, 1, 1, 74, 74, 74, 74] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 216
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042430 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 33, 62, 67, 74, 74, 67, 67, 185, 200, 201, 201, 199, 74, 74, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 33, 33, 66, 66, 67, 67, 74, 74, 200, 200, 201, 201, 74, 74, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 556
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042430 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042430
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042430/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042430
Building REAL300000042431
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042431'
/scratch/stefan/7769623/working/building/REAL300000042431 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042431

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042431/0 /scratch/stefan/7769623/working/building/REAL300000042431 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/474
`/scratch/stefan/7769623/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CC2(CC(N=NC3=CC=CC(C(=O)[O-])=C3)C2)C1)

`REAL300000042431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042431 none CC(C)(C)OC(=O)N1CC2(CC(N=NC3=CC=CC(C(=O)[O-])=C3)C2)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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [25, 19, 26, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 54, 54, 54, 54, 1, 1, 1, 1] 171
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 45, 46, 44, 43, 23, 24, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042431 none CC(C)(C)OC(=O)N1CC2(CC(N=NC3=CC=CC(C(=O)[O-])=C3)C2)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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [171, 171, 171, 171, 107, 54, 107, 54, 54, 54, 54, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 171, 171, 171, 171, 171, 171, 171, 171, 171, 54, 54, 54, 54, 54, 1, 1, 1, 1, 54, 54, 54, 54] 171
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 388
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042431 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042431
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042431/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042431
Building REAL300000042432
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042432'
/scratch/stefan/7769623/working/building/REAL300000042432 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042432

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042432/0 /scratch/stefan/7769623/working/building/REAL300000042432 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/475
`/scratch/stefan/7769623/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C1)

`REAL300000042432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042432 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [47, 39, 47, 47, 11, 6, 11, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 55, 55, 55, 55, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 1, 1, 1, 1, 55, 55, 55, 55, 1, 1] 174
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 184
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042432 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 174, 174, 174, 160, 130, 160, 55, 55, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 174, 174, 174, 174, 174, 174, 174, 174, 174, 130, 55, 55, 55, 55, 1, 1, 1, 1, 55, 55] 174
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 493
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042432 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042432
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042432/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042432
Building REAL300000042433
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042433'
/scratch/stefan/7769623/working/building/REAL300000042433 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042433

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042433/0 /scratch/stefan/7769623/working/building/REAL300000042433 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/476
`/scratch/stefan/7769623/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1)

`REAL300000042433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042433 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 35, 35, 13, 18, 89, 120, 159, 165, 189, 193, 199, 35, 35, 21, 21, 21, 20, 20, 3, 1, 1, 1, 1, 35, 35, 116, 116, 158, 159, 165, 165, 189, 189, 35, 35] 201
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 13, 36, 37] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 836
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042433 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 1, 7, 7, 22, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 6, 10, 24, 26, 45, 53, 55, 1, 1, 11, 11, 11, 11, 11, 22, 35, 35, 35, 35, 1, 1, 10, 10, 24, 24, 27, 27, 44, 44, 1, 1] 201
rigid atoms, others: [48, 2, 49, 38, 39, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 341
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042433 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042433
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042433/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042433
Building REAL300000042434
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042434'
/scratch/stefan/7769623/working/building/REAL300000042434 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042434

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042434/0 /scratch/stefan/7769623/working/building/REAL300000042434 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/477
`/scratch/stefan/7769623/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(F)C=C2)S1)

`REAL300000042434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042434 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(F)C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 51, 51, 51, 10, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100, 100] 100
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 154
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: REAL300000042434 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(F)C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 3, 27, 27, 79, 100, 100, 100, 100, 100, 100, 100, 100, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 28, 79, 100, 100, 100, 100, 4, 4, 4, 1, 1, 1, 1] 100
rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 254
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042434 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=C(F)C=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 54, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 10, 10, 10, 54, 100, 100, 100, 100, 2, 2, 2, 3, 3, 3, 3] 100
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 223
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042434 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042434
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042434/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042434
Building REAL300000042435
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042435'
/scratch/stefan/7769623/working/building/REAL300000042435 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042435

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042435/0 /scratch/stefan/7769623/working/building/REAL300000042435 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/478
`/scratch/stefan/7769623/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C2=NC(C)=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1)

`REAL300000042435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042435 none COC1=CC=C(C2=NC(C)=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 116, 180, 180, 180, 180, 180, 180, 180, 180, 4, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 32, 32, 32, 116, 180, 180, 180, 180, 1, 1] 180
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 423
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: REAL300000042435 none COC1=CC=C(C2=NC(C)=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 60, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 61, 61, 61, 12, 1, 1, 1, 1, 180, 180] 180
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 266
number of broken/clashed sets: 82
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042435 none COC1=CC=C(C2=NC(C)=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [4, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 53, 180, 180, 180, 180, 180, 180, 180, 180, 1, 4, 4, 5, 5, 5, 4, 4, 2, 2, 2, 10, 10, 10, 53, 180, 180, 180, 180, 4, 4] 180
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 24] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 316
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042435 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042435
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042435/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042435
Building REAL300000042436
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042436'
/scratch/stefan/7769623/working/building/REAL300000042436 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042436

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042436/0 /scratch/stefan/7769623/working/building/REAL300000042436 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/479
`/scratch/stefan/7769623/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2)S1)

`REAL300000042436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042436 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 47, 47, 47, 12, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92] 92
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 151
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: REAL300000042436 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 4, 26, 26, 72, 92, 92, 92, 92, 92, 92, 92, 92, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 26, 26, 26, 72, 92, 92, 92, 92, 4, 4, 4, 1, 1, 1, 1, 1] 92
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 229
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042436 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 46, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 10, 10, 10, 46, 92, 92, 92, 92, 2, 2, 2, 4, 4, 2, 4, 4] 92
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 206
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042436 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042436
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042436/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042436
Building REAL300000042437
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042437'
/scratch/stefan/7769623/working/building/REAL300000042437 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042437

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042437/0 /scratch/stefan/7769623/working/building/REAL300000042437 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/480
`/scratch/stefan/7769623/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1N)

`REAL300000042437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042437 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 93, 93, 93, 93, 93, 92, 93, 93, 93, 52, 52, 52, 12, 1, 1, 1, 1, 93, 93, 93, 93, 93] 93
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35])
total number of confs: 156
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042437 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC([N+](=O)[O-])=CC=C1N NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [10, 1, 10, 10, 54, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 54, 93, 93, 93, 93, 1, 1, 1, 2, 2] 93
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 193
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042437 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042437
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042437/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042437
Building REAL300000042438
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042438'
/scratch/stefan/7769623/working/building/REAL300000042438 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042438

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042438/0 /scratch/stefan/7769623/working/building/REAL300000042438 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/481
`/scratch/stefan/7769623/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(CCC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042438 none COC1=CC=C(C(CCC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 41, 42, 61, 62, 12, 12, 77, 153, 153, 153, 153, 153, 153, 153, 153, 1, 1, 2, 2, 2, 1, 1, 41, 41, 42, 42, 62, 61, 62, 62, 62, 62, 62, 77, 153, 153, 153, 153, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 558
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042438 none COC1=CC=C(C(CCC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 80, 50, 153, 153, 29, 29, 29, 83, 83, 92, 97, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 153, 153, 153, 153, 153, 153, 153, 83, 83, 83, 83, 97, 92, 97, 97, 97, 97, 97, 8, 1, 1, 1, 1, 153, 153] 201
rigid atoms, others: [45, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47])
total number of confs: 854
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042438 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042438
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042438/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042438
Building REAL300000042439
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042439'
/scratch/stefan/7769623/working/building/REAL300000042439 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042439

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042439/0 /scratch/stefan/7769623/working/building/REAL300000042439 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/482
`/scratch/stefan/7769623/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2F)S1)

`REAL300000042439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042439 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 102, 102, 102, 102, 102, 201, 201, 156, 201, 201, 201, 102, 36, 36, 36, 8, 1, 1, 1, 1, 102, 102, 102, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
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: REAL300000042439 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 63, 63, 175, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 63, 63, 63, 175, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 499
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042439 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(C2=CC=CC=C2F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 15, 14, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 46, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 12, 12, 2, 12, 12, 12, 1, 10, 10, 10, 46, 102, 102, 102, 102, 2, 2, 2, 12, 12, 12, 12] 201
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 239
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042439 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042439
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042439/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042439
Building REAL300000042440
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042440'
/scratch/stefan/7769623/working/building/REAL300000042440 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042440

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042440/0 /scratch/stefan/7769623/working/building/REAL300000042440 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/483
`/scratch/stefan/7769623/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(=O)[O-])=C1)

`REAL300000042440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042440 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 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: [22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 41, 41, 41, 41, 41, 41, 41, 23, 23, 23, 6, 1, 1, 1, 1, 41, 41] 41
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 73
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042440 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 1, 11, 11, 33, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 33, 41, 41, 41, 41, 1, 1] 41
rigid atoms, others: [1, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 96
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042440 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042440
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042440/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042440
Building REAL300000042441
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042441'
/scratch/stefan/7769623/working/building/REAL300000042441 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042441

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042441/0 /scratch/stefan/7769623/working/building/REAL300000042441 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/484
`/scratch/stefan/7769623/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(C2=CC=CC=C2)=CS1)

`REAL300000042441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042441 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(C2=CC=CC=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 154, 154, 154, 201, 201, 201, 201, 201, 154, 154, 36, 36, 36, 36, 1, 1, 1, 1, 201, 201, 201, 201, 201, 154] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 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: REAL300000042441 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(C2=CC=CC=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 46, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 46, 46, 46, 46, 201, 201, 201, 201, 1, 1, 1, 1, 1, 7] 201
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37])
total number of confs: 378
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042441 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(C2=CC=CC=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 66, 66, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 11, 11, 11, 11, 155, 155, 155, 155, 7, 7, 2, 7, 7, 1] 201
rigid atoms, others: [1, 37, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042441 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042441
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042441/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042441
Building REAL300000042442
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042442'
/scratch/stefan/7769623/working/building/REAL300000042442 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042442

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042442/0 /scratch/stefan/7769623/working/building/REAL300000042442 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/485
`/scratch/stefan/7769623/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@@H+]1CC1=CC=CC=C1)

`REAL300000042442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042442 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 4, 5, 5, 4, 5, 5, 2, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5] 30
rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 61
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: REAL300000042442 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1] 30
rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 50
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042442 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 27, 27, 27, 27, 30, 30, 30, 30, 30, 30, 27, 27, 27, 27, 27, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 30, 30, 30, 30, 30, 30, 30] 30
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 81
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042442 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042442/1 /scratch/stefan/7769623/working/building/REAL300000042442 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/486
`/scratch/stefan/7769623/working/3D/486' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@H+]1CC1=CC=CC=C1)

`REAL300000042442.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042442/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042442 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 4, 5, 5, 4, 5, 5, 2, 2, 2, 1, 1, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 4, 5, 5] 30
rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 35, 29, 30, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 59
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: REAL300000042442 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1] 30
rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 50
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042442 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CCC[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 30, 30, 30, 30, 30, 30, 27, 27, 27, 27, 27, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 30, 30, 30, 30, 30, 30, 30] 30
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 76
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042442 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042442
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042442/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042442/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042442
Building REAL300000042443
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042443'
/scratch/stefan/7769623/working/building/REAL300000042443 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042443

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042443/0 /scratch/stefan/7769623/working/building/REAL300000042443 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/487
`/scratch/stefan/7769623/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(CC2=CC=CC=C2)S1)

`REAL300000042443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042443 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(CC2=CC=CC=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 81, 81, 81, 81, 81, 193, 201, 201, 201, 201, 201, 81, 25, 25, 25, 4, 1, 1, 1, 1, 81, 81, 81, 193, 193, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 607
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: REAL300000042443 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(CC2=CC=CC=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 17, 77, 77, 170, 201, 201, 201, 201, 201, 201, 201, 201, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 17, 77, 77, 77, 170, 201, 201, 201, 201, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 506
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042443 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)N=C(CC2=CC=CC=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 42, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 7, 18, 18, 12, 18, 18, 1, 10, 10, 10, 42, 81, 81, 81, 81, 2, 2, 2, 7, 7, 18, 18, 18, 18, 18] 201
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 237
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042443 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042443
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042443/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042443
Building REAL300000042444
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042444'
/scratch/stefan/7769623/working/building/REAL300000042444 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042444

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042444/0 /scratch/stefan/7769623/working/building/REAL300000042444 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/488
`/scratch/stefan/7769623/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=C(Cl)C=CC=C1Cl)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042444 none CC(CC1=C(Cl)C=CC=C1Cl)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 9, 4, 4, 1, 1, 1, 39, 39, 39, 39] 39
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042444 none CC(CC1=C(Cl)C=CC=C1Cl)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [29, 8, 29, 39, 39, 39, 39, 39, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 29, 39, 39, 39, 39, 39, 1, 1, 1, 1] 39
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042444 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042444
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042444/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042444
Building REAL300000042445
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042445'
/scratch/stefan/7769623/working/building/REAL300000042445 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042445

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042445/0 /scratch/stefan/7769623/working/building/REAL300000042445 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/489
`/scratch/stefan/7769623/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=C(F)C=C1Br)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042445 none CC(CC1=CC=C(F)C=C1Br)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 17, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 89, 89, 129, 129, 129, 129, 129, 129, 129, 129, 18, 18, 18, 18, 8, 8, 1, 1, 1, 129, 129, 129, 129] 129
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 230
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042445 none CC(CC1=CC=C(F)C=C1Br)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 17, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [45, 9, 45, 84, 129, 129, 129, 129, 129, 129, 129, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 84, 84, 129, 129, 129, 1, 1, 1, 1] 129
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 422
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042445 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042445
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042445/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042445
Building REAL300000042446
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042446'
/scratch/stefan/7769623/working/building/REAL300000042446 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042446

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042446/0 /scratch/stefan/7769623/working/building/REAL300000042446 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/490
`/scratch/stefan/7769623/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1)

`REAL300000042446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042446 none O=C([O-])C1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 46, 46, 46, 46, 46, 56, 56, 56, 56, 56, 46, 1, 1, 1, 1, 46, 46, 46, 56, 56, 56, 56, 56, 46, 46, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 120
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: REAL300000042446 none O=C([O-])C1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 33, 33, 6, 6, 6, 1, 6, 8, 8, 1, 1, 1, 1, 1, 1, 6, 56, 56, 56, 56, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 56] 56
rigid atoms, others: [32, 33, 34, 12, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 91
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042446 none O=C([O-])C1=CC=CC(N=NC2CC(C(=O)[O-])(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [46, 46, 46, 46, 46, 46, 46, 13, 13, 1, 1, 1, 1, 1, 3, 3, 1, 6, 6, 2, 6, 6, 1, 46, 46, 46, 46, 1, 1, 1, 6, 6, 3, 6, 6, 1, 1, 46] 56
rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 16, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34, 37])
total number of confs: 82
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042446 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042446
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042446/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042446
Building REAL300000042447
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042447'
/scratch/stefan/7769623/working/building/REAL300000042447 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042447

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042447/0 /scratch/stefan/7769623/working/building/REAL300000042447 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/491
`/scratch/stefan/7769623/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(F)C=C3)C2)=C1)

`REAL300000042447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042447 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(F)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 39, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 92
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: REAL300000042447 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(F)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 22, 22, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 41] 41
rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 62
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042447 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=C(F)C=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 41] 41
rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 21, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 32, 33, 34, 35, 38])
total number of confs: 59
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042447 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042447
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042447/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042447
Building REAL300000042448
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042448'
/scratch/stefan/7769623/working/building/REAL300000042448 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042448

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042448/0 /scratch/stefan/7769623/working/building/REAL300000042448 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/492
`/scratch/stefan/7769623/working/3D/492' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=C(N)C(F)=C1)

`REAL300000042448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042448 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=C(N)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 51, 51, 51, 39, 39, 51, 51, 51, 39, 39, 39, 10, 1, 1, 1, 1, 51, 51, 51, 51] 51
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 178
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042448 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=C(N)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 32, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 51, 51, 51, 51, 1, 2, 2, 1] 51
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 112
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042448 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042448
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042448/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042448
Building REAL300000042449
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042449'
/scratch/stefan/7769623/working/building/REAL300000042449 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042449

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042449/0 /scratch/stefan/7769623/working/building/REAL300000042449 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/493
`/scratch/stefan/7769623/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(N)=C1)

`REAL300000042449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042449 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 156, 156, 156, 156, 156, 156, 156, 93, 93, 93, 92, 92, 10, 1, 1, 1, 1, 156, 156, 156, 156, 156] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36])
total number of confs: 455
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042449 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 13, 1, 13, 13, 74, 156, 156, 156, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 74, 156, 156, 156, 156, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 391
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042449 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042449
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042449/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042449
Building REAL300000042450
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042450'
/scratch/stefan/7769623/working/building/REAL300000042450 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042450

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042450/0 /scratch/stefan/7769623/working/building/REAL300000042450 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/494
`/scratch/stefan/7769623/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C)

`REAL300000042450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042450 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 22, 22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 21, 21, 21, 21, 1, 1, 1, 1, 22, 22, 26, 26, 22, 22, 22, 22, 22, 22] 26
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042450 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 4, 4, 4, 4, 22, 22, 22, 22, 1, 1, 5, 5, 2, 2, 2, 2, 2, 2] 26
rigid atoms, others: [1, 34, 33, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042450 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042450
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042450/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042450
Building REAL300000042451
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042451'
/scratch/stefan/7769623/working/building/REAL300000042451 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042451

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042451/0 /scratch/stefan/7769623/working/building/REAL300000042451 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/495
`/scratch/stefan/7769623/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042451 none CC(CCCCCCC(=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 74, 80, 104, 130, 149, 197, 200, 200, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 36, 78, 78, 80, 80, 108, 108, 130, 130, 156, 156, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 1055
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042451 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042451
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042451/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042451
Building REAL300000042452
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042452'
/scratch/stefan/7769623/working/building/REAL300000042452 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042452

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042452/0 /scratch/stefan/7769623/working/building/REAL300000042452 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/496
`/scratch/stefan/7769623/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CC(C)N=NC2=CC=CC(C(=O)[O-])=C2)C(C)=C1OC)

`REAL300000042452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042452 none COC1=CC=C(CC(C)N=NC2=CC=CC(C(=O)[O-])=C2)C(C)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 10, 10, 68, 68, 144, 144, 144, 144, 144, 144, 144, 144, 1, 1, 1, 1, 5, 4, 4, 4, 1, 1, 4, 4, 10, 10, 10, 10, 144, 144, 144, 144, 2, 2, 2, 5, 5, 5] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 254
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042452 none COC1=CC=C(CC(C)N=NC2=CC=CC(C(=O)[O-])=C2)C(C)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 144, 144, 144, 144, 91, 42, 8, 42, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 144, 144, 144, 144, 201, 201, 201, 201, 144, 144, 91, 91, 42, 42, 42, 42, 1, 1, 1, 1, 144, 144, 144, 201, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45])
total number of confs: 696
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042452 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042452
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042452/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042452
Building REAL300000042453
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042453'
/scratch/stefan/7769623/working/building/REAL300000042453 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042453

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042453/0 /scratch/stefan/7769623/working/building/REAL300000042453 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/497
`/scratch/stefan/7769623/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC(CC3=CC=CC=C3)C2)=C1)

`REAL300000042453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042453 none O=C([O-])C1=CC=CC(N=NC2CCC(CC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 34, 64, 64, 64, 64, 64, 64, 34, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 64, 64, 64, 64, 64, 64, 64, 34, 34, 1] 64
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042453 none O=C([O-])C1=CC=CC(N=NC2CCC(CC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 64, 64, 64, 64, 64, 64, 36, 36, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 8, 64, 64, 64, 64, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 8, 8, 64] 64
rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 113
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042453 none O=C([O-])C1=CC=CC(N=NC2CCC(CC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 34, 34, 34, 13, 13, 1, 1, 1, 1, 1, 1, 5, 8, 8, 5, 8, 8, 1, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 1, 1, 34] 64
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 21, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 41])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042453 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042453
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042453/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042453
Building REAL300000042454
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042454'
/scratch/stefan/7769623/working/building/REAL300000042454 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042454

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042454/0 /scratch/stefan/7769623/working/building/REAL300000042454 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/498
`/scratch/stefan/7769623/working/3D/498' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=N1)

`REAL300000042454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042454 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [60, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 60, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 60, 60, 60, 60, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141] 141
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042454 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [26, 4, 26, 106, 106, 141, 141, 141, 141, 141, 141, 141, 141, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 26, 26, 26, 26, 141, 141, 141, 141, 4, 1, 1, 1, 1, 1] 141
rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 247
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042454 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CN(C2=CC=CC=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 84, 84, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 13, 13, 13, 13, 141, 141, 141, 141, 1, 4, 4, 1, 4, 4] 141
rigid atoms, others: [32, 1, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 229
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042454 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042454
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042454/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042454
Building REAL300000042455
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042455'
/scratch/stefan/7769623/working/building/REAL300000042455 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042455

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042455/0 /scratch/stefan/7769623/working/building/REAL300000042455 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/499
`/scratch/stefan/7769623/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)SC2=C(Cl)C=CC=C12)

`REAL300000042455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042455 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)SC2=C(Cl)C=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 11, 11, 59, 91, 91, 91, 91, 91, 92, 92, 91, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 59, 91, 91, 91, 91, 1, 1, 1] 92
rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042455 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)SC2=C(Cl)C=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [91, 91, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 91, 91, 91, 91, 91, 91, 91, 91, 92, 92, 92, 53, 12, 1, 1, 1, 1, 91, 91, 91] 92
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 150
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042455 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042455
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042455/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042455
Building REAL300000042456
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042456'
/scratch/stefan/7769623/working/building/REAL300000042456 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042456

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042456/0 /scratch/stefan/7769623/working/building/REAL300000042456 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/500
`/scratch/stefan/7769623/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1CCCN1C(=O)OC(C)(C)C)

`REAL300000042456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042456 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1CCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [41, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 60, 60, 60, 60, 60, 60, 110, 110, 136, 136, 136, 136, 41, 41, 41, 41, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 136, 136, 136, 136, 136, 136, 136, 136, 136] 136
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 417
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042456 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@@H]1CCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 21, 21, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 22, 22, 22, 4, 4, 4, 4, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 136
rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042456 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042456
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042456/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042456
Building REAL300000042457
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042457'
/scratch/stefan/7769623/working/building/REAL300000042457 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042457

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042457/0 /scratch/stefan/7769623/working/building/REAL300000042457 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/501
`/scratch/stefan/7769623/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCN1C(=O)OC(C)(C)C)

`REAL300000042457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042457 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 63, 63, 63, 63, 63, 63, 108, 108, 138, 138, 138, 138, 50, 50, 50, 50, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 138, 138, 138, 138, 138, 138, 138, 138, 138] 138
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 414
number of broken/clashed sets: 123
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042457 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)[C@H]1CCCN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 24, 24, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 22, 22, 22, 5, 5, 5, 5, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 138
rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 152
number of broken/clashed sets: 123
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042457 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042457
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042457/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042457
Building REAL300000042458
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042458'
/scratch/stefan/7769623/working/building/REAL300000042458 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042458

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042458/0 /scratch/stefan/7769623/working/building/REAL300000042458 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/502
`/scratch/stefan/7769623/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Br)NN=C2Br)=C1)

`REAL300000042458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042458 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)NN=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 8, 1, 17, 1, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 31, 31, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 12, 31, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042458 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)NN=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'N.2', 'C.2', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 8, 1, 17, 1, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 40, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 40, 13, 1, 48] 48
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 25])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042458 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042458
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042458/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042458
Building REAL300000042459
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042459'
/scratch/stefan/7769623/working/building/REAL300000042459 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042459

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042459/0 /scratch/stefan/7769623/working/building/REAL300000042459 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/503
`/scratch/stefan/7769623/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=C(F)C=C2O)=C1)

`REAL300000042459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042459 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=C(F)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 9, 31, 34, 34, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 122
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042459 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=C(F)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [34, 34, 34, 34, 34, 34, 34, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 27, 8, 1, 1, 2, 34] 68
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 81
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042459 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042459/1 /scratch/stefan/7769623/working/building/REAL300000042459 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/504
`/scratch/stefan/7769623/working/3D/504' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=C(F)C=C2[O-])=C1)

`REAL300000042459.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042459/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042459 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=C(F)C=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 22
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042459 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=C(F)C=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 10, 4, 1, 1, 11] 11
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042459 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042459
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042459/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042459/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042459
Building REAL300000042460
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042460'
/scratch/stefan/7769623/working/building/REAL300000042460 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042460

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042460/0 /scratch/stefan/7769623/working/building/REAL300000042460 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/505
`/scratch/stefan/7769623/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CC=C12)

`REAL300000042460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042460 none COC1=CC=CC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 61, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 1, 1, 3, 4, 3, 1, 1, 1, 12, 61, 143, 143, 143, 143, 1, 1, 1] 143
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 20, 21, 22, 23, 36, 27, 28, 29, 37] set([0, 32, 34, 35, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31])
total number of confs: 265
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042460 none COC1=CC=CC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 143, 143, 143, 143, 67, 67, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 67, 12, 1, 1, 1, 1, 143, 143, 143] 143
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 208
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042460 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042460
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042460/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042460
Building REAL300000042461
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042461'
/scratch/stefan/7769623/working/building/REAL300000042461 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042461

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042461/0 /scratch/stefan/7769623/working/building/REAL300000042461 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/506
`/scratch/stefan/7769623/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCCOC2=O)C=C1)

`REAL300000042461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042461 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCCOC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 11, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 83, 83, 70, 81, 146, 146, 146, 146, 146, 146, 83, 83, 45, 45, 45, 10, 1, 1, 1, 1, 83, 83, 146, 146, 146, 146, 146, 146, 83, 83] 146
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 309
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: REAL300000042461 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCCOC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 11, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [26, 3, 25, 26, 92, 146, 146, 146, 146, 146, 146, 146, 146, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 26, 26, 92, 146, 146, 146, 146, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8] 146
rigid atoms, others: [36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
total number of confs: 334
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042461 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2CCCOC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 11, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 28, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 6, 6, 6, 28, 83, 83, 83, 83, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1] 146
rigid atoms, others: [1, 34, 35, 42, 43, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
total number of confs: 154
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042461 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042461
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042461/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042461
Building REAL300000042462
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042462'
/scratch/stefan/7769623/working/building/REAL300000042462 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042462

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042462/0 /scratch/stefan/7769623/working/building/REAL300000042462 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/507
`/scratch/stefan/7769623/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC=C(Cl)C=C32)=C1)

`REAL300000042462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042462 none O=C([O-])C1=CC=CC(NN=C2COC3=CC=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 11, 23, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042462 none O=C([O-])C1=CC=CC(NN=C2COC3=CC=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042462 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042462
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042462/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042462
Building REAL300000042463
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042463'
/scratch/stefan/7769623/working/building/REAL300000042463 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042463

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042463/0 /scratch/stefan/7769623/working/building/REAL300000042463 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/508
`/scratch/stefan/7769623/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC=C(Br)C=C32)=C1)

`REAL300000042463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042463 none O=C([O-])C1=CC=CC(NN=C2COC3=CC=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 11, 23, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042463 none O=C([O-])C1=CC=CC(NN=C2COC3=CC=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042463 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042463
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042463/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042463
Building REAL300000042464
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042464'
/scratch/stefan/7769623/working/building/REAL300000042464 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042464

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042464/0 /scratch/stefan/7769623/working/building/REAL300000042464 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/509
`/scratch/stefan/7769623/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=C(Cl)C=CC=C23)=C1)

`REAL300000042464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042464 none O=C([O-])C1=CC=CC(NN=C2COC3=C(Cl)C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 11, 27, 26, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 11, 27, 27, 27, 27, 27, 1] 27
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042464 none O=C([O-])C1=CC=CC(NN=C2COC3=C(Cl)C=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 26, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 26, 27, 27, 9, 1, 1, 1, 1, 1, 27] 27
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042464 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042464
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042464/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042464
Building REAL300000042465
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042465'
/scratch/stefan/7769623/working/building/REAL300000042465 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042465

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042465/0 /scratch/stefan/7769623/working/building/REAL300000042465 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/510
`/scratch/stefan/7769623/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Cl)=CC2=C1OCC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042465 none CC1=CC(Cl)=CC2=C1OCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 21, 21, 20, 2, 2, 2, 1, 1, 1, 1, 9, 20, 20, 20, 20] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042465 none CC1=CC(Cl)=CC2=C1OCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 20, 20, 20, 20, 8, 1, 1, 1, 1] 21
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042465 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042465
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042465/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042465
Building REAL300000042466
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042466'
/scratch/stefan/7769623/working/building/REAL300000042466 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042466

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042466/0 /scratch/stefan/7769623/working/building/REAL300000042466 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/511
`/scratch/stefan/7769623/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=C2OCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1)

`REAL300000042466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042466 none CC1=CC(Br)=C2OCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 22, 22, 21, 1, 1, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 21, 1] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 20, 21, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042466 none CC1=CC(Br)=C2OCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 22, 22, 22, 21, 21, 21, 8, 1, 1, 1, 1, 21] 22
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 46
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042466 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042466
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042466/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042466
Building REAL300000042467
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042467'
/scratch/stefan/7769623/working/building/REAL300000042467 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042467

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042467/0 /scratch/stefan/7769623/working/building/REAL300000042467 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/512
`/scratch/stefan/7769623/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=C(Br)C=C(Cl)C=C23)=C1)

`REAL300000042467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042467 none O=C([O-])C1=CC=CC(NN=C2COC3=C(Br)C=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042467 none O=C([O-])C1=CC=CC(NN=C2COC3=C(Br)C=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 17, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 9, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042467 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042467
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042467/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042467
Building REAL300000042468
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042468'
/scratch/stefan/7769623/working/building/REAL300000042468 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042468

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042468/0 /scratch/stefan/7769623/working/building/REAL300000042468 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/513
`/scratch/stefan/7769623/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC(OCC4=CC=CC=C4)=CC=C32)=C1)

`REAL300000042468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042468 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(OCC4=CC=CC=C4)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 38, 39, 39, 39, 39, 39, 76, 121, 121, 121, 121, 121, 121, 39, 39, 33, 1, 1, 1, 1, 9, 39, 39, 39, 121, 121, 121, 121, 121, 121, 121, 39, 39, 1] 121
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 44, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 346
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: REAL300000042468 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(OCC4=CC=CC=C4)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 121, 121, 121, 120, 121, 121, 85, 39, 39, 39, 39, 40, 39, 39, 15, 3, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 121, 121, 121, 121, 85, 40, 40, 40, 3, 3, 1, 1, 1, 1, 1, 39, 39, 121] 121
rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 258
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042468 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(OCC4=CC=CC=C4)=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 38, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 22, 39, 39, 24, 39, 39, 1, 1, 1, 39, 38, 39, 39, 9, 1, 1, 1, 22, 22, 39, 39, 39, 39, 39, 1, 1, 39] 121
rigid atoms, others: [32, 33, 34, 43, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 44])
total number of confs: 210
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042468 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042468
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042468/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042468
Building REAL300000042469
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042469'
/scratch/stefan/7769623/working/building/REAL300000042469 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042469

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042469/0 /scratch/stefan/7769623/working/building/REAL300000042469 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/514
`/scratch/stefan/7769623/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1)

`REAL300000042469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042469 none COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 111, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 155, 155, 92, 155, 155, 155, 133, 133, 133, 111, 111, 7, 1, 1, 1, 1, 155, 155, 155, 155] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 795
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042469 none COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 59, 12, 1, 12, 12, 80, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 59, 59, 80, 155, 155, 155, 155, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 547
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042469 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042469
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042469/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042469
Building REAL300000042470
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042470'
/scratch/stefan/7769623/working/building/REAL300000042470 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042470

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042470/0 /scratch/stefan/7769623/working/building/REAL300000042470 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/515
`/scratch/stefan/7769623/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1)

`REAL300000042470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042470 none COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [144, 132, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 126, 126, 69, 126, 126, 126, 144, 144, 144, 132, 132, 10, 1, 1, 1, 1, 126, 126, 126, 126] 146
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 764
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042470 none COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [72, 36, 7, 1, 7, 7, 43, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 36, 36, 43, 126, 126, 126, 126, 1, 1, 1, 1] 146
rigid atoms, others: [32, 33, 34, 3, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 375
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042470 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042470
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042470/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042470
Building REAL300000042471
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042471'
/scratch/stefan/7769623/working/building/REAL300000042471 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042471

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042471/0 /scratch/stefan/7769623/working/building/REAL300000042471 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/516
`/scratch/stefan/7769623/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC(F)=CC(F)=C32)=C1)

`REAL300000042471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042471 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(F)=CC(F)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 11, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042471 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(F)=CC(F)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 9, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 30])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042471 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042471
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042471/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042471
Building REAL300000042472
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042472'
/scratch/stefan/7769623/working/building/REAL300000042472 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042472

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042472/0 /scratch/stefan/7769623/working/building/REAL300000042472 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/517
`/scratch/stefan/7769623/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1)

`REAL300000042472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042472 none CSCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [172, 117, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 115, 115, 39, 38, 115, 115, 115, 115, 115, 172, 172, 172, 117, 117, 8, 1, 1, 1, 1, 115, 115, 115, 115] 190
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 14, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 1039
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042472 none CSCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [95, 32, 6, 1, 6, 6, 42, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 95, 95, 95, 32, 32, 42, 115, 115, 115, 115, 1, 1, 1, 1] 190
rigid atoms, others: [19, 3, 36, 37, 38, 15, 16, 17, 18, 35, 23, 24] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 394
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042472 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042472
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042472/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042472
Building REAL300000042473
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042473'
/scratch/stefan/7769623/working/building/REAL300000042473 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042473

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042473/0 /scratch/stefan/7769623/working/building/REAL300000042473 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/518
`/scratch/stefan/7769623/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)COC2=C1OC)

`REAL300000042473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042473 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)COC2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 58, 58, 58, 58, 58, 59, 59, 58, 1, 1, 1, 1, 1, 7, 4, 4, 4, 1, 1, 9, 58, 58, 58, 58, 1, 1, 7, 7, 7] 99
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 18, 19, 20, 21, 22, 27, 28, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042473 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)COC2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [99, 58, 58, 58, 58, 52, 58, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 58, 58, 58, 58, 99, 99, 99, 99, 58, 58, 10, 1, 1, 1, 1, 58, 58, 99, 99, 99] 99
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042473 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042473
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042473/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042473
Building REAL300000042474
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042474'
/scratch/stefan/7769623/working/building/REAL300000042474 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042474

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042474/0 /scratch/stefan/7769623/working/building/REAL300000042474 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/519
`/scratch/stefan/7769623/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC=CC(Cl)=C32)=C1)

`REAL300000042474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042474 none O=C([O-])C1=CC=CC(NN=C2COC3=CC=CC(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 9, 21, 20, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042474 none O=C([O-])C1=CC=CC(NN=C2COC3=CC=CC(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 20, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 20, 21, 21, 9, 1, 1, 1, 1, 1, 21] 21
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042474 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042474
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042474/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042474
Building REAL300000042475
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042475'
/scratch/stefan/7769623/working/building/REAL300000042475 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042475

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042475/0 /scratch/stefan/7769623/working/building/REAL300000042475 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/520
`/scratch/stefan/7769623/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC3=C(C2)C2=CC=CC=C2N3)=C1)

`REAL300000042475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042475 none O=C([O-])C1=CC=CC(N=NC2CC3=C(C2)C2=CC=CC=C2N3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042475 none O=C([O-])C1=CC=CC(N=NC2CC3=C(C2)C2=CC=CC=C2N3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 36])
total number of confs: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042475 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042475
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042475/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042475
Building REAL300000042476
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042476'
/scratch/stefan/7769623/working/building/REAL300000042476 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042476

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042476/0 /scratch/stefan/7769623/working/building/REAL300000042476 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/521
`/scratch/stefan/7769623/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC(F)=C(Br)C=C32)=C1)

`REAL300000042476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042476 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(F)=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 11, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042476 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(F)=C(Br)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 15, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 9, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042476 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042476
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042476/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042476
Building REAL300000042477
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042477'
/scratch/stefan/7769623/working/building/REAL300000042477 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042477

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042477/0 /scratch/stefan/7769623/working/building/REAL300000042477 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/522
`/scratch/stefan/7769623/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2COC3=CC(Br)=CN=C32)=C1)

`REAL300000042477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042477 none O=C([O-])C1=CC=CC(N=NC2COC3=CC(Br)=CN=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 18, 18, 18, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042477 none O=C([O-])C1=CC=CC(N=NC2COC3=CC(Br)=CN=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 1, 1, 1, 1, 1, 18] 18
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29])
total number of confs: 23
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042477 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042477
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042477/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042477
Building REAL300000042478
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042478'
/scratch/stefan/7769623/working/building/REAL300000042478 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042478

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042478/0 /scratch/stefan/7769623/working/building/REAL300000042478 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/523
`/scratch/stefan/7769623/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F)

`REAL300000042478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042478 none COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [169, 152, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 138, 138, 138, 138, 138, 138, 138, 169, 169, 169, 152, 152, 10, 1, 1, 1, 1, 138, 138, 138] 186
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 618
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042478 none COCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [79, 40, 11, 1, 11, 11, 51, 138, 138, 138, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 40, 40, 51, 138, 138, 138, 138, 1, 1, 1] 186
rigid atoms, others: [33, 34, 3, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 408
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042478 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042478
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042478/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042478
Building REAL300000042479
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042479'
/scratch/stefan/7769623/working/building/REAL300000042479 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042479

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042479/0 /scratch/stefan/7769623/working/building/REAL300000042479 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/524
`/scratch/stefan/7769623/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2COC3=CC(Br)=C(F)C=C32)=C1)

`REAL300000042479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042479 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(Br)=C(F)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 11, 23, 23, 23, 23, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042479 none O=C([O-])C1=CC=CC(NN=C2COC3=CC(Br)=C(F)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 22, 23, 23, 9, 1, 1, 1, 1, 23] 23
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 30])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042479 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042479
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042479/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042479
Building REAL300000042480
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042480'
/scratch/stefan/7769623/working/building/REAL300000042480 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042480

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042480/0 /scratch/stefan/7769623/working/building/REAL300000042480 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/525
`/scratch/stefan/7769623/working/3D/525' -> `0.mol2'
Preparing input files

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

`REAL300000042480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042480 none CC(CC1=CC=C(Br)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 53, 53, 87, 87, 87, 87, 87, 87, 87, 87, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 87, 87, 87, 87] 87
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042480 none CC(CC1=CC=C(Br)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [45, 8, 45, 83, 87, 87, 83, 83, 87, 87, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 83, 83, 87, 87, 87, 87, 1, 1, 1, 1] 87
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 351
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042480 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042480
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042480/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042480
Building REAL300000042481
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042481'
/scratch/stefan/7769623/working/building/REAL300000042481 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042481

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042481/0 /scratch/stefan/7769623/working/building/REAL300000042481 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/526
`/scratch/stefan/7769623/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OCCCC(=O)[O-])

`REAL300000042481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042481 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 10, 10, 21, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 9, 27, 34, 48, 62, 62, 4, 4, 4, 1, 10, 10, 10, 21, 34, 34, 34, 34, 1, 1, 27, 27, 34, 34, 48, 48] 201
rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 18, 19, 20, 21, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 337
number of broken/clashed sets: 91
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042481 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OCCCC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 34, 34, 34, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 34, 110, 163, 172, 201, 201, 201, 60, 60, 60, 34, 14, 14, 14, 3, 1, 1, 1, 1, 34, 34, 163, 163, 172, 172, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 660
number of broken/clashed sets: 91
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042481 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042481
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042481/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042481
Building REAL300000042482
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042482'
/scratch/stefan/7769623/working/building/REAL300000042482 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042482

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042482/0 /scratch/stefan/7769623/working/building/REAL300000042482 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/527
`/scratch/stefan/7769623/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(N)=C1)

`REAL300000042482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042482 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 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: [49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 98, 98, 98, 98, 98, 98, 98, 50, 50, 50, 10, 1, 1, 1, 1, 98, 98, 98, 98, 98] 98
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33])
total number of confs: 159
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042482 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C(N)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 53, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 98, 98, 98, 98, 1, 1, 2, 2, 1] 98
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 204
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042482 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042482
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042482/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042482
Building REAL300000042483
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042483'
/scratch/stefan/7769623/working/building/REAL300000042483 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042483

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042483/0 /scratch/stefan/7769623/working/building/REAL300000042483 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/528
`/scratch/stefan/7769623/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OCC(=O)N(C)C)

`REAL300000042483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042483 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OCC(=O)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 49, 49, 32, 49, 49, 49, 105, 185, 199, 199, 199, 199, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 49, 49, 49, 49, 185, 185, 199, 199, 199, 199, 199, 199] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 13, 36] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 744
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042483 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OCC(=O)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 1, 7, 7, 27, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 8, 34, 58, 58, 58, 58, 15, 15, 15, 15, 15, 27, 49, 49, 49, 49, 1, 1, 1, 1, 34, 34, 58, 58, 58, 58, 58, 58] 201
rigid atoms, others: [2, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 325
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042483 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042483
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042483/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042483
Building REAL300000042484
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042484'
/scratch/stefan/7769623/working/building/REAL300000042484 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042484

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042484/0 /scratch/stefan/7769623/working/building/REAL300000042484 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/529
`/scratch/stefan/7769623/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(SC3=CC=CC=C3)S2)=C1)

`REAL300000042484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042484 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(SC3=CC=CC=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 42, 42, 42, 42, 42, 201, 201, 201, 201, 201, 201, 42, 1, 1, 1, 1, 9, 27, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 265
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042484 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(SC3=CC=CC=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 183, 88, 88, 37, 37, 37, 37, 37, 6, 1, 1, 1, 1, 1, 1, 1, 37, 201, 201, 201, 201, 183, 88, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 501
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042484 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(SC3=CC=CC=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 14, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 22, 37, 37, 1, 42, 42, 42, 42, 24, 6, 37, 37, 22, 37, 37, 42] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042484 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042484
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042484/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042484
Building REAL300000042485
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042485'
/scratch/stefan/7769623/working/building/REAL300000042485 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042485

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042485/0 /scratch/stefan/7769623/working/building/REAL300000042485 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/530
`/scratch/stefan/7769623/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042485 none COC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 44, 44, 137, 201, 201, 201, 201, 201, 201, 201, 201, 1, 3, 3, 3, 1, 1, 1, 11, 11, 44, 137, 201, 201, 201, 201, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 24, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 438
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: REAL300000042485 none COC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 71, 71, 71, 71, 71, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 71, 71, 26, 7, 1, 1, 1, 1, 201] 201
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 289
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042485 none COC1=CC=CC(C2=NNC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 38, 71, 71, 71, 71, 71, 71, 71, 71, 11, 21, 21, 21, 11, 11, 11, 1, 1, 11, 38, 71, 71, 71, 71, 11] 201
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 174
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042485 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042485
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042485/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042485
Building REAL300000042486
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042486'
/scratch/stefan/7769623/working/building/REAL300000042486 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042486

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042486/0 /scratch/stefan/7769623/working/building/REAL300000042486 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/531
`/scratch/stefan/7769623/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(Cl)N2C2=CC=CC=C2)=C1)

`REAL300000042486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042486 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(Cl)N2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 63, 63, 182, 182, 182, 182, 182, 182, 182, 188, 188, 188, 188, 188, 1, 1, 1, 1, 13, 63, 188, 188, 188, 188, 188, 1] 188
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042486 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(Cl)N2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 188, 188, 188, 188, 188, 131, 37, 37, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 131, 37, 1, 1, 1, 1, 1, 188] 188
rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 35])
total number of confs: 421
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042486 none O=C([O-])C1=CC=CC(NN=CC2=C(Cl)N=C(Cl)N2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 16, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [182, 182, 182, 182, 182, 182, 182, 89, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 182, 182, 182, 182, 89, 12, 6, 6, 2, 6, 6, 182] 188
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 361
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042486 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042486
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042486/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042486
Building REAL300000042487
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042487'
/scratch/stefan/7769623/working/building/REAL300000042487 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042487

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042487/0 /scratch/stefan/7769623/working/building/REAL300000042487 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/532
`/scratch/stefan/7769623/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2N2C=NC=N2)=C1)

`REAL300000042487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042487 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2N2C=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 1] 3
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 7
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042487 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2N2C=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 3] 3
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, 34])
total number of confs: 12
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042487 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2N2C=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3] 3
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 9
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042487 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042487
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042487/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042487
Building REAL300000042488
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042488'
/scratch/stefan/7769623/working/building/REAL300000042488 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042488

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042488/0 /scratch/stefan/7769623/working/building/REAL300000042488 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/533
`/scratch/stefan/7769623/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC2=CC=CC=C2N=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042488 none CC1=NC2=CC=CC=C2N=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 60, 94, 94, 94, 94, 94, 95, 95, 94, 2, 2, 2, 1, 1, 1, 1, 11, 60, 94, 94, 94, 94] 95
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 211
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042488 none CC1=NC2=CC=CC=C2N=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 95, 95, 95, 94, 94, 94, 94, 54, 12, 1, 1, 1, 1] 95
rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042488 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042488
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042488/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042488
Building REAL300000042489
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042489'
/scratch/stefan/7769623/working/building/REAL300000042489 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042489

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042489/0 /scratch/stefan/7769623/working/building/REAL300000042489 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/534
`/scratch/stefan/7769623/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1(C)C)

`REAL300000042489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042489 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1(C)C 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 17, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 1, 1, 1, 1, 1, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2] 88
rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 22, 23, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042489 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1(C)C 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 61, 35, 61, 35, 35, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 88, 88, 88, 88, 88, 88, 88, 88, 88, 35, 35, 35, 35, 35, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35] 88
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042489 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042489
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042489/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042489
Building REAL300000042490
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042490'
/scratch/stefan/7769623/working/building/REAL300000042490 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042490

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042490/0 /scratch/stefan/7769623/working/building/REAL300000042490 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/535
`/scratch/stefan/7769623/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1)

`REAL300000042490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042490 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 60, 60, 60, 60, 185, 201, 201, 185, 201, 201, 60, 60, 37, 37, 37, 8, 1, 1, 1, 1, 60, 60, 201, 201, 185, 201, 201, 59] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 350
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: REAL300000042490 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 19, 54, 54, 154, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 54, 54, 54, 154, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 1, 19] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 482
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042490 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 25, 60, 60, 60, 60, 60, 61, 61, 60, 1, 1, 1, 1, 1, 9, 19, 19, 9, 19, 19, 1, 1, 6, 6, 6, 25, 60, 60, 60, 60, 1, 1, 19, 19, 9, 19, 19, 1] 201
rigid atoms, others: [1, 34, 35, 41, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 170
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042490 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042490/1 /scratch/stefan/7769623/working/building/REAL300000042490 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/536
`/scratch/stefan/7769623/working/3D/536' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1)

`REAL300000042490.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042490/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042490 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 72, 72, 72, 72, 195, 201, 201, 195, 201, 201, 72, 72, 26, 26, 26, 26, 1, 1, 1, 1, 72, 72, 201, 201, 195, 201, 201, 72] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042490 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 18, 66, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 66, 66, 66, 66, 201, 201, 201, 201, 18, 18, 1, 1, 1, 1, 1, 18] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 431
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042490 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 38, 38, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 9, 18, 18, 9, 18, 18, 1, 1, 9, 9, 9, 9, 72, 72, 72, 72, 1, 1, 18, 18, 9, 18, 18, 1] 201
rigid atoms, others: [1, 34, 35, 41, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40])
total number of confs: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042490 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042490
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042490/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042490/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042490
Building REAL300000042491
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042491'
/scratch/stefan/7769623/working/building/REAL300000042491 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042491

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042491/0 /scratch/stefan/7769623/working/building/REAL300000042491 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/537
`/scratch/stefan/7769623/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)CCC(CC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042491 none CC(C)(C)OC(=O)CCC(CC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 75, 16, 75, 10, 5, 2, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 41, 41, 41, 41, 41, 41, 41, 41, 83, 83, 83, 83, 83, 83, 83, 83, 83, 16, 16, 10, 10, 5, 2, 2, 1, 1, 1, 1, 1, 41, 41, 41, 41] 201
rigid atoms, others: [48, 47, 12, 10, 11, 44, 13, 14, 45, 16, 46, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 49, 50, 51, 52])
total number of confs: 291
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042491 none CC(C)(C)OC(=O)CCC(CC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [177, 177, 177, 177, 169, 57, 169, 32, 22, 6, 22, 41, 41, 41, 41, 41, 41, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 177, 177, 177, 177, 177, 177, 177, 177, 177, 51, 57, 38, 38, 22, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1] 201
rigid atoms, others: [51, 50, 49, 18, 19, 20, 21, 22, 23, 24, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 702
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042491 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042491
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042491/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042491
Building REAL300000042492
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042492'
/scratch/stefan/7769623/working/building/REAL300000042492 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042492

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042492/0 /scratch/stefan/7769623/working/building/REAL300000042492 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/538
`/scratch/stefan/7769623/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)(CN=NC1=CC=CC(C(=O)[O-])=C1)CNC(=O)OC(C)(C)C)

`REAL300000042492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042492 none CCC(CC)(CN=NC1=CC=CC(C(=O)[O-])=C1)CNC(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 48, 16, 48, 59, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 93, 160, 197, 197, 200, 200, 200, 200, 60, 60, 60, 59, 57, 57, 59, 60, 60, 60, 16, 16, 1, 1, 1, 1, 91, 91, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 16, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 923
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042492 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042492
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042492/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042492
Building REAL300000042493
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042493'
/scratch/stefan/7769623/working/building/REAL300000042493 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042493

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042493/0 /scratch/stefan/7769623/working/building/REAL300000042493 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/539
`/scratch/stefan/7769623/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042493 none CN1N=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 6, 7, 7, 7, 26, 26, 68, 78, 78, 78, 78, 78, 78, 78, 78, 2, 2, 2, 1, 1, 7, 7, 7, 7, 26, 68, 78, 78, 78, 78] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042493 none CN1N=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 78, 63, 63, 63, 63, 63, 63, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 78, 78, 78, 78, 78, 63, 63, 63, 63, 30, 7, 1, 1, 1, 1] 78
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 129
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042493 none CN1N=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 63, 63, 63, 63, 63, 63, 63, 63, 7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 37, 63, 63, 63, 63] 78
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 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: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042493 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042493
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042493/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042493
Building REAL300000042494
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042494'
/scratch/stefan/7769623/working/building/REAL300000042494 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042494

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042494/0 /scratch/stefan/7769623/working/building/REAL300000042494 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/540
`/scratch/stefan/7769623/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C[NH+](C)C)C=C1)

`REAL300000042494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042494 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C[NH+](C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 115, 115, 89, 115, 146, 146, 146, 146, 115, 115, 51, 51, 51, 10, 1, 1, 1, 1, 115, 115, 146, 146, 146, 146, 146, 146, 146, 146, 115, 115] 146
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 497
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042494 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C[NH+](C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 37, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 7, 7, 7, 37, 115, 115, 115, 115, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 1] 146
rigid atoms, others: [32, 1, 33, 42, 43, 13, 14, 15, 16, 17, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 232
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042494 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042494
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042494/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042494
Building REAL300000042495
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042495'
/scratch/stefan/7769623/working/building/REAL300000042495 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042495

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042495/0 /scratch/stefan/7769623/working/building/REAL300000042495 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/541
`/scratch/stefan/7769623/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(C[NH+](C)C)=C1)

`REAL300000042495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042495 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 40, 40, 40, 40, 40, 50, 50, 50, 50, 40, 23, 23, 23, 6, 1, 1, 1, 1, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 40] 50
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 134
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042495 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 1, 9, 9, 20, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 1, 9, 9, 9, 20, 40, 40, 40, 40, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 1] 50
rigid atoms, others: [32, 1, 34, 33, 43, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 112
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042495 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042495
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042495/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042495
Building REAL300000042496
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042496'
/scratch/stefan/7769623/working/building/REAL300000042496 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042496

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042496/0 /scratch/stefan/7769623/working/building/REAL300000042496 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/542
`/scratch/stefan/7769623/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C)

`REAL300000042496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042496 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 10, 10, 45, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 10, 10, 10, 1, 1, 10, 44, 67, 67, 67, 66, 2, 2, 2] 97
rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042496 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 66, 96, 66, 66, 66, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 67, 97, 97, 97, 66, 66, 32, 8, 1, 1, 1, 1, 67, 67, 67] 97
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042496 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042496
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042496/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042496
Building REAL300000042497
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042497'
/scratch/stefan/7769623/working/building/REAL300000042497 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042497

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042497/0 /scratch/stefan/7769623/working/building/REAL300000042497 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/543
`/scratch/stefan/7769623/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC[NH+]1C2CCC1CC(N=NC1=CC=CC(C(=O)[O-])=C1)C2)

`REAL300000042497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042497 none COCC[NH+]1C2CCC1CC(N=NC1=CC=CC(C(=O)[O-])=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 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, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [11, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 11, 11, 11, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1] 23
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43])
total number of confs: 49
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042497 none COCC[NH+]1C2CCC1CC(N=NC1=CC=CC(C(=O)[O-])=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 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, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 17, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 23, 23, 23, 23, 23, 17, 17, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10] 23
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45])
total number of confs: 91
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042497 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042497
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042497/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042497
Building REAL300000042498
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042498'
/scratch/stefan/7769623/working/building/REAL300000042498 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042498

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042498/0 /scratch/stefan/7769623/working/building/REAL300000042498 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/544
`/scratch/stefan/7769623/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(S(=O)(=O)CC(N)=O)C=C1)

`REAL300000042498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042498 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(S(=O)(=O)CC(N)=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 1, 8, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 89, 89, 54, 89, 113, 113, 113, 185, 201, 201, 89, 89, 31, 31, 31, 6, 1, 1, 1, 1, 89, 89, 185, 185, 201, 201, 89, 89] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 857
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042498 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(S(=O)(=O)CC(N)=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 1, 8, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 34, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 2, 2, 2, 18, 53, 53, 1, 1, 6, 6, 6, 34, 89, 89, 89, 89, 1, 1, 18, 18, 53, 51, 1, 1] 201
rigid atoms, others: [1, 34, 35, 40, 41, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 320
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042498 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042498
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042498/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042498
Building REAL300000042499
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042499'
/scratch/stefan/7769623/working/building/REAL300000042499 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042499

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042499/0 /scratch/stefan/7769623/working/building/REAL300000042499 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/545
`/scratch/stefan/7769623/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)C=CC2=C1CCCC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042499 none CN1C(=O)C=CC2=C1CCCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22] 22
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 33] set([34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 44
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042499 none CN1C(=O)C=CC2=C1CCCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1] 22
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 42
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042499 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042499
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042499/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042499
Building REAL300000042500
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042500'
/scratch/stefan/7769623/working/building/REAL300000042500 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042500

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042500/0 /scratch/stefan/7769623/working/building/REAL300000042500 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/546
`/scratch/stefan/7769623/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC3=C(F)C(F)=CC=C3C=C2)=C1)

`REAL300000042500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042500 none O=C([O-])C1=CC=CC(NN=CC2=NC3=C(F)C(F)=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 11, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 11, 29, 30, 30, 30, 30, 1] 30
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042500 none O=C([O-])C1=CC=CC(NN=CC2=NC3=C(F)C(F)=CC=C3C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 15, 1, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 16, 4, 1, 1, 1, 1, 30] 30
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 23, 24, 25, 26, 27, 28])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042500 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042500
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042500/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042500
Building REAL300000042501
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042501'
/scratch/stefan/7769623/working/building/REAL300000042501 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042501

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042501/0 /scratch/stefan/7769623/working/building/REAL300000042501 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/547
`/scratch/stefan/7769623/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=NN=C2)=C1)

`REAL300000042501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042501 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 151, 151, 151, 151, 151, 151, 151, 151, 151, 151, 49, 49, 49, 10, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151] 151
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 222
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: REAL300000042501 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [38, 9, 38, 38, 99, 145, 145, 145, 145, 145, 145, 145, 145, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 99, 145, 145, 145, 145, 8, 9, 9, 1, 1, 9] 145
rigid atoms, others: [35, 36, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37])
total number of confs: 330
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042501 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 76, 151, 151, 151, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 11, 11, 11, 76, 151, 151, 151, 151, 1, 1, 1, 6, 6, 1] 151
rigid atoms, others: [32, 1, 34, 37, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36])
total number of confs: 300
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042501 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042501
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042501/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042501
Building REAL300000042502
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042502'
/scratch/stefan/7769623/working/building/REAL300000042502 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042502

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042502/0 /scratch/stefan/7769623/working/building/REAL300000042502 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/548
`/scratch/stefan/7769623/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Cl)C2=COC=C2)=C1)

`REAL300000042502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042502 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 88, 129, 129, 88, 129, 129, 129, 19, 60, 60, 60, 60, 1, 1, 1, 1, 6, 88, 88, 129, 129, 115, 129, 60, 60, 60, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042502 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 24, 8, 8, 1, 8, 53, 92, 92, 53, 92, 92, 92, 1, 1, 1, 1, 1, 60, 60, 60, 60, 24, 53, 53, 92, 92, 80, 92, 1, 1, 1, 60] 201
rigid atoms, others: [35, 36, 37, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 485
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042502 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 129, 129, 129, 129, 129, 83, 33, 33, 6, 1, 1, 1, 1, 1, 1, 1, 1, 33, 92, 92, 92, 92, 129, 129, 129, 129, 83, 6, 6, 1, 1, 1, 1, 92, 92, 92, 129] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 395
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042502 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042502
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042502/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042502
Building REAL300000042503
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042503'
/scratch/stefan/7769623/working/building/REAL300000042503 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042503

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042503/0 /scratch/stefan/7769623/working/building/REAL300000042503 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/549
`/scratch/stefan/7769623/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2=C(F)C=CC=C2Cl)C2=COC=C2)=C1)

`REAL300000042503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042503 none O=C([O-])C1=CC=CC(NN=C(CC2=C(F)C=CC=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 89, 134, 134, 134, 89, 134, 134, 134, 19, 51, 51, 51, 51, 1, 1, 1, 1, 6, 89, 89, 134, 129, 134, 51, 51, 51, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042503 none O=C([O-])C1=CC=CC(NN=C(CC2=C(F)C=CC=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 26, 9, 9, 1, 9, 57, 99, 99, 99, 57, 99, 99, 99, 1, 1, 1, 1, 1, 51, 51, 51, 51, 26, 57, 57, 99, 93, 99, 1, 1, 1, 51] 201
rigid atoms, others: [35, 36, 37, 10, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 538
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042503 none O=C([O-])C1=CC=CC(NN=C(CC2=C(F)C=CC=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [134, 134, 134, 134, 134, 134, 134, 83, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 99, 99, 99, 99, 134, 134, 134, 134, 83, 5, 5, 1, 1, 1, 99, 99, 99, 134] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 405
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042503 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042503
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042503/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042503
Building REAL300000042504
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042504'
/scratch/stefan/7769623/working/building/REAL300000042504 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042504

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042504/0 /scratch/stefan/7769623/working/building/REAL300000042504 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/550
`/scratch/stefan/7769623/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Br)C2=COC=C2)=C1)

`REAL300000042504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042504 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Br)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 89, 138, 138, 89, 138, 138, 138, 19, 60, 60, 60, 60, 1, 1, 1, 1, 6, 89, 89, 138, 138, 121, 138, 60, 60, 60, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 613
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042504 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Br)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 27, 8, 8, 1, 8, 53, 96, 96, 53, 96, 96, 96, 1, 1, 1, 1, 1, 60, 60, 60, 60, 27, 53, 53, 96, 96, 78, 96, 1, 1, 1, 60] 201
rigid atoms, others: [35, 36, 37, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 497
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042504 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=CC=C2Br)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 138, 138, 138, 138, 92, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 96, 96, 96, 96, 138, 138, 138, 138, 92, 6, 6, 1, 1, 1, 1, 96, 96, 96, 138] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 416
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042504 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042504
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042504/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042504
Building REAL300000042505
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042505'
/scratch/stefan/7769623/working/building/REAL300000042505 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042505

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042505/0 /scratch/stefan/7769623/working/building/REAL300000042505 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/551
`/scratch/stefan/7769623/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2=CC=C(F)C=C2Cl)C2=COC=C2)=C1)

`REAL300000042505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042505 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=C(F)C=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 87, 129, 129, 114, 117, 129, 129, 129, 19, 56, 56, 56, 56, 1, 1, 1, 1, 6, 87, 87, 129, 129, 129, 56, 56, 56, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 458
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042505 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=C(F)C=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 24, 8, 8, 1, 8, 48, 82, 82, 70, 72, 82, 82, 82, 1, 1, 1, 1, 1, 56, 56, 56, 56, 24, 48, 48, 82, 82, 82, 1, 1, 1, 56] 201
rigid atoms, others: [35, 36, 37, 10, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 349
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042505 none O=C([O-])C1=CC=CC(NN=C(CC2=CC=C(F)C=C2Cl)C2=COC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 1, 1, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 129, 129, 129, 129, 129, 83, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 82, 82, 82, 82, 129, 129, 129, 129, 83, 6, 6, 1, 1, 1, 82, 82, 82, 129] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042505 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042505
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042505/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042505
Building REAL300000042506
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042506'
/scratch/stefan/7769623/working/building/REAL300000042506 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042506

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042506/0 /scratch/stefan/7769623/working/building/REAL300000042506 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/552
`/scratch/stefan/7769623/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC(F)=CC(F)=C3)C2)=C1)

`REAL300000042506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042506 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC(F)=CC(F)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 33, 33, 57, 57, 57, 57, 57, 57, 57, 33, 1, 1, 1, 1, 33, 33, 33, 33, 57, 57, 57, 33, 33, 1] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 117
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: REAL300000042506 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC(F)=CC(F)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 57, 57, 32, 32, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 57, 57, 57, 57, 7, 7, 7, 7, 1, 1, 1, 7, 7, 57] 57
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 90
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042506 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC(F)=CC(F)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 33, 33, 33, 33, 33, 12, 12, 1, 1, 1, 1, 1, 7, 7, 7, 1, 7, 7, 7, 1, 33, 33, 33, 33, 1, 1, 1, 1, 7, 5, 7, 1, 1, 33] 57
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 35])
total number of confs: 65
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042506 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042506
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042506/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042506
Building REAL300000042507
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042507'
/scratch/stefan/7769623/working/building/REAL300000042507 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042507

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042507/0 /scratch/stefan/7769623/working/building/REAL300000042507 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/553
`/scratch/stefan/7769623/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(C(=O)[O-])=C1)=C2CC(=O)[O-])

`REAL300000042507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042507 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(C(=O)[O-])=C1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 11, 11, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 5, 5, 37, 37, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 67, 67, 67, 67, 2, 2] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042507 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC(C(=O)[O-])=C1)=C2CC(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 11, 11, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 2, 2, 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: [67, 67, 67, 67, 67, 67, 67, 67, 38, 8, 38, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 72, 72, 72, 67, 67, 67, 67, 67, 67, 38, 38, 38, 38, 1, 1, 1, 1, 72, 72] 72
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 200
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042507 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042507
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042507/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042507
Building REAL300000042508
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042508'
/scratch/stefan/7769623/working/building/REAL300000042508 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042508

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042508/0 /scratch/stefan/7769623/working/building/REAL300000042508 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/554
`/scratch/stefan/7769623/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C2CCCC2=CC2=C1CCC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042508 none NC1=C2CCCC2=CC2=C1CCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 5, 5, 5, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 21, 21, 20, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042508 none NC1=C2CCCC2=CC2=C1CCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 5, 5, 5, 1, 1, 1, 1, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1] 21
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042508 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042508
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042508/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042508
Building REAL300000042509
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042509'
/scratch/stefan/7769623/working/building/REAL300000042509 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042509

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042509/0 /scratch/stefan/7769623/working/building/REAL300000042509 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/555
`/scratch/stefan/7769623/working/3D/555' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(Cl)=NC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042509 none CN1C(Cl)=NC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 16, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 10, 27, 42, 42, 42, 42] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042509 none CN1C(Cl)=NC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 16, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 42, 42, 42, 42, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 42, 42, 34, 10, 1, 1, 1, 1] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042509 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042509
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042509/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042509
Building REAL300000042510
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042510'
/scratch/stefan/7769623/working/building/REAL300000042510 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042510

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042510/0 /scratch/stefan/7769623/working/building/REAL300000042510 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/556
`/scratch/stefan/7769623/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C)

`REAL300000042510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042510 none COC1=NC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 30, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 5, 5, 5, 11, 30, 37, 37, 37, 37, 2, 2, 2] 37
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20] set([0, 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: 99
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042510 none COC1=NC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 37, 37, 37, 37, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 37, 18, 6, 1, 1, 1, 1, 37, 37, 37] 37
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042510 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042510
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042510/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042510
Building REAL300000042511
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042511'
/scratch/stefan/7769623/working/building/REAL300000042511 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042511

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042511/0 /scratch/stefan/7769623/working/building/REAL300000042511 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/557
`/scratch/stefan/7769623/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CON=C2CC2=CC=CC=C2)=C1)

`REAL300000042511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042511 none O=C([O-])C1=CC=CC(NN=CC2=CON=C2CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 93, 93, 93, 93, 93, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 13, 37, 93, 195, 195, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042511 none O=C([O-])C1=CC=CC(NN=CC2=CON=C2CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 166, 56, 56, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 166, 56, 15, 4, 4, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37])
total number of confs: 480
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042511 none O=C([O-])C1=CC=CC(NN=CC2=CON=C2CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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: [93, 93, 93, 93, 92, 93, 93, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 9, 15, 15, 93, 92, 93, 93, 49, 8, 1, 7, 7, 15, 15, 15, 15, 15, 93] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042511 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042511
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042511/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042511
Building REAL300000042512
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042512'
/scratch/stefan/7769623/working/building/REAL300000042512 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042512

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042512/0 /scratch/stefan/7769623/working/building/REAL300000042512 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/558
`/scratch/stefan/7769623/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(=O)N(C)C)C=C1)

`REAL300000042512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042512 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 44, 44, 33, 44, 55, 55, 55, 55, 44, 44, 20, 20, 20, 3, 1, 1, 1, 1, 44, 44, 55, 55, 55, 55, 55, 55, 44, 44] 55
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 173
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042512 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 26, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 5, 5, 5, 26, 44, 44, 44, 44, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 55
rigid atoms, others: [32, 1, 33, 40, 41, 13, 14, 15, 16, 17, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 108
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042512 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042512
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042512/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042512
Building REAL300000042513
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042513'
/scratch/stefan/7769623/working/building/REAL300000042513 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042513

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042513/0 /scratch/stefan/7769623/working/building/REAL300000042513 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/559
`/scratch/stefan/7769623/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC3=C(CCCC3)S2)=C1)

`REAL300000042513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042513 none O=C([O-])C1=CC=CC(N=NCC2=NC3=C(CCCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 47, 46, 117, 117, 117, 117, 117, 117, 117, 117, 1] 117
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 23] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042513 none O=C([O-])C1=CC=CC(N=NCC2=NC3=C(CCCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 117, 117, 117, 117, 117, 117, 68, 68, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 117] 117
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25])
total number of confs: 175
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042513 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042513/1 /scratch/stefan/7769623/working/building/REAL300000042513 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/560
`/scratch/stefan/7769623/working/3D/560' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC3=C(CCCC3)S2)=C1)

`REAL300000042513.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042513/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042513 none O=C([O-])C1=CC=CC(NN=CC2=NC3=C(CCCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 11, 35, 44, 44, 44, 44, 44, 44, 44, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 23] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042513 none O=C([O-])C1=CC=CC(NN=CC2=NC3=C(CCCC3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 5, 5, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 43, 44, 44, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 43, 44, 44, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 44] 44
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 22, 23, 24, 25])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042513 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042513
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042513/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042513/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042513
Building REAL300000042514
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042514'
/scratch/stefan/7769623/working/building/REAL300000042514 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042514

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042514/0 /scratch/stefan/7769623/working/building/REAL300000042514 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/561
`/scratch/stefan/7769623/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N(C)C2=CC=CC=C12)

`REAL300000042514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042514 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N(C)C2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 12, 12, 48, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 48, 57, 57, 57, 57, 2, 2, 2, 1, 1, 1, 1] 57
rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 15, 16, 17, 18, 19, 20, 21, 22, 38] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042514 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N(C)C2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 40, 12, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57] 57
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042514 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042514
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042514/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042514
Building REAL300000042515
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042515'
/scratch/stefan/7769623/working/building/REAL300000042515 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042515

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042515/0 /scratch/stefan/7769623/working/building/REAL300000042515 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/562
`/scratch/stefan/7769623/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NC=C(Br)S2)=C1)

`REAL300000042515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042515 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(Br)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 88, 88, 88, 88, 88, 1, 1, 1, 1, 40, 41, 88, 1] 88
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042515 none O=C([O-])C1=CC=CC(N=NCC2=NC=C(Br)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 58, 58, 8, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 8, 8, 1, 88] 88
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 24])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042515 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042515/1 /scratch/stefan/7769623/working/building/REAL300000042515 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/563
`/scratch/stefan/7769623/working/3D/563' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)S2)=C1)

`REAL300000042515.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042515/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042515 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 32, 32, 40, 40, 40, 40, 40, 1, 1, 1, 1, 11, 32, 40, 1] 40
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042515 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 14, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 7, 7, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 29, 7, 1, 40] 40
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 24])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042515 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042515
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042515/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042515/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042515
Building REAL300000042516
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042516'
/scratch/stefan/7769623/working/building/REAL300000042516 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042516

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042516/0 /scratch/stefan/7769623/working/building/REAL300000042516 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/564
`/scratch/stefan/7769623/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042516 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 45, 55, 55, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 2, 2, 2, 1, 13, 45, 55, 55, 55, 55] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 145
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042516 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 55, 55, 55, 55, 55, 55, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 55, 55, 55, 55, 55, 55, 31, 7, 1, 1, 1, 1] 55
rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042516 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042516
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042516/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042516
Building REAL300000042517
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042517'
/scratch/stefan/7769623/working/building/REAL300000042517 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042517

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042517/0 /scratch/stefan/7769623/working/building/REAL300000042517 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/565
`/scratch/stefan/7769623/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O)

`REAL300000042517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042517 none CC1=CC(Br)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 2, 2, 2, 1, 1, 9, 28, 41, 41, 41, 41, 2] 82
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 99
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042517 none CC1=CC(Br)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [41, 41, 41, 41, 41, 41, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 41, 41, 32, 9, 1, 1, 1, 1, 82] 82
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 152
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042517 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042517
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042517/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042517
Building REAL300000042518
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042518'
/scratch/stefan/7769623/working/building/REAL300000042518 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042518

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042518/0 /scratch/stefan/7769623/working/building/REAL300000042518 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/566
`/scratch/stefan/7769623/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC2=C(C1)SC(CN=NC1=CC=CC(C(=O)[O-])=C1)=N2)

`REAL300000042518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042518 none CC1CCC2=C(C1)SC(CN=NC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 5, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 69, 69, 125, 125, 125, 125, 125, 125, 125, 125, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 125, 125, 125, 125] 125
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042518 none CC1CCC2=C(C1)SC(CN=NC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 5, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 125, 125, 125, 125, 125, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 44, 44, 1, 1, 1, 1] 125
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042518 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042518/1 /scratch/stefan/7769623/working/building/REAL300000042518 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/567
`/scratch/stefan/7769623/working/3D/567' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC2=C(C1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=N2)

`REAL300000042518.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042518/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042518 none CC1CCC2=C(C1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 5, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 43, 43, 43, 43, 43, 44, 44, 43, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 8, 33, 43, 43, 43, 43] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042518 none CC1CCC2=C(C1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 5, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 43, 43, 43, 43, 43, 43, 43, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 44, 44, 44, 43, 43, 43, 43, 43, 43, 43, 32, 8, 1, 1, 1, 1] 44
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042518 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042518
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042518/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042518/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042518
Building REAL300000042519
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042519'
/scratch/stefan/7769623/working/building/REAL300000042519 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042519

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042519/0 /scratch/stefan/7769623/working/building/REAL300000042519 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/568
`/scratch/stefan/7769623/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC2=C(C1)SC(CN=NC1=CC=CC(C(=O)[O-])=C1)=N2)

`REAL300000042519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042519 none CC1(C)CCC2=C(C1)SC(CN=NC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 5, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 68, 68, 136, 136, 136, 136, 136, 136, 136, 136, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 136, 136, 136, 136] 136
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 22, 33, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 219
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042519 none CC1(C)CCC2=C(C1)SC(CN=NC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 5, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 136, 136, 136, 136, 136, 136, 136, 136, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 45, 45, 1, 1, 1, 1] 136
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 272
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042519 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042519/1 /scratch/stefan/7769623/working/building/REAL300000042519 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/569
`/scratch/stefan/7769623/working/3D/569' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC2=C(C1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=N2)

`REAL300000042519.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042519/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042519 none CC1(C)CCC2=C(C1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 5, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 44, 44, 44, 44, 44, 45, 45, 44, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 31, 44, 44, 44, 44] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 32, 22, 33, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042519 none CC1(C)CCC2=C(C1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=N2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 5, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 45, 45, 45, 45, 45, 45, 44, 44, 44, 44, 44, 44, 34, 9, 1, 1, 1, 1] 45
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042519 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042519
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042519/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042519/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042519
Building REAL300000042520
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042520'
/scratch/stefan/7769623/working/building/REAL300000042520 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042520

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042520/0 /scratch/stefan/7769623/working/building/REAL300000042520 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/570
`/scratch/stefan/7769623/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)SC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21)

`REAL300000042520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042520 none CN1C(=O)SC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 14, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 48, 70, 70, 70, 70, 70, 71, 71, 70, 1, 1, 1, 2, 2, 2, 1, 8, 48, 70, 70, 70, 70, 1, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 20, 21, 22, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042520 none CN1C(=O)SC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 14, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 70, 71, 71, 71, 70, 40, 12, 1, 1, 1, 1, 70, 70] 71
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 131
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042520 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042520
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042520/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042520
Building REAL300000042521
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042521'
/scratch/stefan/7769623/working/building/REAL300000042521 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042521

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042521/0 /scratch/stefan/7769623/working/building/REAL300000042521 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/571
`/scratch/stefan/7769623/working/3D/571' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1)

`REAL300000042521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042521 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 7, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 7, 19, 21, 21, 21, 1] 21
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 36
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042521 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 21, 21, 21, 21, 16, 4, 1, 1, 1, 21] 21
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042521 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042521
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042521/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042521
Building REAL300000042522
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042522'
/scratch/stefan/7769623/working/building/REAL300000042522 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042522

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042522/0 /scratch/stefan/7769623/working/building/REAL300000042522 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/572
`/scratch/stefan/7769623/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042522 none CC(C)(C)C1=CN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 9, 59, 59, 135, 135, 135, 135, 135, 135, 135, 135, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 9, 9, 135, 135, 135, 135] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042522 none CC(C)(C)C1=CN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 135, 201, 201, 135, 135, 135, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 50, 50, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 681
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042522 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042522/1 /scratch/stefan/7769623/working/building/REAL300000042522 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/573
`/scratch/stefan/7769623/working/3D/573' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042522.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042522/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042522 none CC(C)(C)C1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 38, 58, 58, 58, 58, 58, 58, 58, 58, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 8, 38, 58, 58, 58, 58] 83
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042522 none CC(C)(C)C1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 58, 83, 83, 58, 58, 58, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 83, 83, 83, 83, 83, 83, 83, 83, 83, 58, 40, 10, 1, 1, 1, 1] 83
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042522 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042522
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042522/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042522/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042522
Building REAL300000042523
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042523'
/scratch/stefan/7769623/working/building/REAL300000042523 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042523

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042523/0 /scratch/stefan/7769623/working/building/REAL300000042523 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/574
`/scratch/stefan/7769623/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2N2C=NC=N2)=C1)

`REAL300000042523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042523 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2N2C=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 1] 3
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 7
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042523 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2N2C=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 3] 3
rigid atoms, others: [32, 33, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 12
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042523 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2N2C=NC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
3  conformations in input
total number of sets (complete confs): 3
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 3] 3
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 9
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042523 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042523
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042523/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042523
Building REAL300000042524
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042524'
/scratch/stefan/7769623/working/building/REAL300000042524 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042524

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042524/0 /scratch/stefan/7769623/working/building/REAL300000042524 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/575
`/scratch/stefan/7769623/working/3D/575' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(=O)CCC2=O)C=C1)

`REAL300000042524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042524 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(=O)CCC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 82, 82, 69, 75, 103, 103, 103, 103, 103, 103, 82, 82, 52, 52, 52, 10, 1, 1, 1, 1, 82, 82, 103, 103, 103, 103, 82, 82] 103
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 239
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042524 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(=O)CCC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [22, 4, 22, 22, 66, 103, 103, 103, 103, 103, 103, 103, 103, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 22, 22, 66, 103, 103, 103, 103, 8, 8, 1, 1, 1, 1, 8, 8] 103
rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 244
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042524 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(N2C(=O)CCC2=O)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 1, 6, 6, 32, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 32, 82, 82, 82, 82, 1, 1, 6, 6, 6, 6, 1, 1] 103
rigid atoms, others: [1, 34, 35, 40, 41, 13, 14, 15, 16, 17, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39])
total number of confs: 153
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042524 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042524
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042524/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042524
Building REAL300000042525
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042525'
/scratch/stefan/7769623/working/building/REAL300000042525 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042525

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042525/0 /scratch/stefan/7769623/working/building/REAL300000042525 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/576
`/scratch/stefan/7769623/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCOCC1)

`REAL300000042525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042525 none CC(C)(C)OC(=O)NCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCOCC1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 37, 39, 39, 27, 17, 27, 7, 1, 1, 1, 8, 41, 41, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17, 7, 7, 8, 8, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [8, 9, 10, 45, 46, 47, 48, 49, 50, 51, 52, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 253
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042525 none CC(C)(C)OC(=O)NCC1(CN=NC2=CC=CC(C(=O)[O-])=C2)CCOCC1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 184, 153, 184, 110, 80, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 80, 80, 80, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 110, 110, 24, 24, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80] 201
rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 696
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042525 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042525
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042525/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042525
Building REAL300000042526
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042526'
/scratch/stefan/7769623/working/building/REAL300000042526 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042526

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042526/0 /scratch/stefan/7769623/working/building/REAL300000042526 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/577
`/scratch/stefan/7769623/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(Br)=C2)=C1)

`REAL300000042526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042526 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 13, 35, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042526 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 26, 6, 1, 1, 1, 33] 33
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042526 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042526
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042526/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042526
Building REAL300000042527
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042527'
/scratch/stefan/7769623/working/building/REAL300000042527 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042527

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042527/0 /scratch/stefan/7769623/working/building/REAL300000042527 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/578
`/scratch/stefan/7769623/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042527 none COCCOCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 78, 52, 17, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 38, 38, 38, 38, 38, 39, 39, 38, 1, 1, 99, 99, 99, 78, 78, 52, 52, 5, 5, 1, 1, 6, 24, 38, 38, 38, 38, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 442
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042527 none COCCOCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 171, 145, 87, 39, 27, 39, 38, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 39, 201, 201, 201, 201, 201, 171, 171, 87, 87, 39, 38, 13, 3, 1, 1, 1, 1, 39, 39] 201
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 753
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042527 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042527
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042527/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042527
Building REAL300000042528
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042528'
/scratch/stefan/7769623/working/building/REAL300000042528 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042528

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042528/0 /scratch/stefan/7769623/working/building/REAL300000042528 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/579
`/scratch/stefan/7769623/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(OC)=C1OCC(F)F)

`REAL300000042528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042528 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(OC)=C1OCC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 23, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 1, 1, 2, 12, 52, 52, 3, 3, 3, 1, 9, 23, 43, 43, 43, 43, 1, 3, 3, 3, 12, 12, 52] 201
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 21, 22, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 291
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042528 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(OC)=C1OCC(F)F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 5, 5, 15, 15, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 43, 43, 43, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 69, 21, 25, 60, 172, 201, 201, 69, 69, 69, 43, 11, 3, 1, 1, 1, 1, 43, 69, 69, 69, 172, 172, 201] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 895
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042528 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042528
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042528/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042528
Building REAL300000042529
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042529'
/scratch/stefan/7769623/working/building/REAL300000042529 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042529

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042529/0 /scratch/stefan/7769623/working/building/REAL300000042529 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/580
`/scratch/stefan/7769623/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2CCOC2)C2=CC=C(F)C=C2)=C1)

`REAL300000042529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042529 none O=C([O-])C1=CC=CC(NN=C(CC2CCOC2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 45, 45, 162, 197, 197, 197, 197, 45, 142, 142, 85, 142, 142, 142, 1, 1, 1, 1, 9, 162, 162, 197, 197, 197, 197, 197, 197, 197, 142, 142, 142, 142, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 1049
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: REAL300000042529 none O=C([O-])C1=CC=CC(NN=C(CC2CCOC2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [142, 142, 142, 142, 142, 142, 142, 42, 6, 6, 1, 6, 30, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 42, 30, 30, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 142] 201
rigid atoms, others: [38, 39, 40, 41, 10, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 420
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042529 none O=C([O-])C1=CC=CC(NN=C(CC2CCOC2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 197, 197, 197, 197, 197, 100, 29, 29, 7, 1, 1, 1, 1, 1, 1, 29, 60, 60, 40, 60, 60, 60, 197, 197, 197, 197, 100, 7, 7, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 197] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42])
total number of confs: 543
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042529 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042529
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042529/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042529
Building REAL300000042530
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042530'
/scratch/stefan/7769623/working/building/REAL300000042530 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042530

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042530/0 /scratch/stefan/7769623/working/building/REAL300000042530 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/581
`/scratch/stefan/7769623/working/3D/581' -> `0.mol2'
Preparing input files

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

`REAL300000042530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042530 none O=C([O-])C1=CC=CC(NN=CC2=CC(O)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 44, 44, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 13, 44, 83, 166, 83, 83, 1] 166
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042530 none O=C([O-])C1=CC=CC(NN=CC2=CC(O)=CC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 83, 83, 83, 83, 51, 9, 1, 2, 1, 1, 83] 166
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 32, 22, 23, 24, 25, 26, 27, 29])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042530 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042530
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042530/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042530
Building REAL300000042531
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042531'
/scratch/stefan/7769623/working/building/REAL300000042531 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042531

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042531/0 /scratch/stefan/7769623/working/building/REAL300000042531 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/582
`/scratch/stefan/7769623/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3Br)N=N2)=C1)

`REAL300000042531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042531 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3Br)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 52, 52, 75, 75, 75, 127, 127, 75, 127, 127, 127, 75, 75, 1, 1, 1, 1, 13, 52, 75, 127, 127, 105, 127, 1] 127
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042531 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3Br)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 127, 127, 127, 127, 127, 127, 102, 31, 31, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 127, 127, 127, 127, 102, 31, 9, 1, 1, 1, 1, 127] 127
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 290
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042531 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3Br)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [75, 75, 75, 75, 75, 75, 75, 37, 8, 8, 1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 1, 1, 75, 75, 75, 75, 37, 8, 1, 9, 9, 1, 9, 75] 127
rigid atoms, others: [10, 11, 12, 13, 14, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042531 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042531/1 /scratch/stefan/7769623/working/building/REAL300000042531 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/583
`/scratch/stefan/7769623/working/3D/583' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3Br)N=N2)=C1)

`REAL300000042531.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042531/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042531 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3Br)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 41, 102, 102, 102, 201, 201, 184, 201, 201, 201, 102, 102, 1, 1, 1, 1, 40, 41, 102, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 452
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042531 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3Br)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 147, 147, 35, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 35, 35, 7, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 349
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042531 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=CC=C3Br)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 102, 102, 102, 102, 102, 49, 49, 8, 1, 1, 1, 1, 1, 7, 7, 3, 7, 7, 7, 1, 1, 102, 102, 102, 102, 8, 8, 1, 7, 7, 3, 7, 102] 201
rigid atoms, others: [10, 11, 12, 13, 14, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042531 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042531
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042531/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042531/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042531
Building REAL300000042532
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042532'
/scratch/stefan/7769623/working/building/REAL300000042532 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042532

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042532/0 /scratch/stefan/7769623/working/building/REAL300000042532 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/584
`/scratch/stefan/7769623/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=CC(C)=C1O)

`REAL300000042532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042532 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=CC(C)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 69, 69, 69, 69, 69, 69, 69, 69, 41, 41, 41, 10, 1, 1, 1, 1, 69, 69, 69, 69, 69, 138] 138
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 256
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042532 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(Cl)=CC(C)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 43, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 43, 69, 69, 69, 69, 1, 1, 2, 2, 2, 2] 138
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 161
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042532 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042532
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042532/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042532
Building REAL300000042533
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042533'
/scratch/stefan/7769623/working/building/REAL300000042533 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042533

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042533/0 /scratch/stefan/7769623/working/building/REAL300000042533 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/585
`/scratch/stefan/7769623/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C12CC3CC(CC(C3)C1)C2)

`REAL300000042533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042533 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C12CC3CC(CC(C3)C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 62
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042533 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C12CC3CC(CC(C3)C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 1, 4, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 21
rigid atoms, others: [2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042533 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042533
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042533/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042533
Building REAL300000042534
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042534'
/scratch/stefan/7769623/working/building/REAL300000042534 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042534

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042534/0 /scratch/stefan/7769623/working/building/REAL300000042534 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/586
`/scratch/stefan/7769623/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+]1CC1=CC=CC=C1)

`REAL300000042534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042534 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 2, 2, 2, 1, 1, 18, 18, 18, 18, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4] 19
rigid atoms, others: [0, 1, 2, 3, 36, 37, 34, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 46
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: REAL300000042534 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 19, 19, 19, 19, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1] 19
rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 35
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042534 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19] 19
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 49
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042534 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042534/1 /scratch/stefan/7769623/working/building/REAL300000042534 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/587
`/scratch/stefan/7769623/working/3D/587' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+]1CC1=CC=CC=C1)

`REAL300000042534.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042534/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042534 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 4, 6, 6, 4, 6, 6, 2, 2, 2, 1, 1, 24, 24, 24, 24, 1, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6] 32
rigid atoms, others: [0, 1, 2, 3, 36, 37, 34, 14, 15, 16, 17, 18, 35, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 60
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: REAL300000042534 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 32, 32, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1] 32
rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 58
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042534 none CC1C(N=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 24, 24, 24, 24, 24, 1, 1, 1, 1, 24, 24, 24, 24, 32, 32, 32, 32, 32, 32, 32] 32
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 91
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042534 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042534
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042534/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042534/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042534
Building REAL300000042535
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042535'
/scratch/stefan/7769623/working/building/REAL300000042535 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042535

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042535/0 /scratch/stefan/7769623/working/building/REAL300000042535 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/588
`/scratch/stefan/7769623/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2NC(=O)C(=O)NC2=C1)

`REAL300000042535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042535 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2NC(=O)C(=O)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [54, 55, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113, 55, 55, 55, 11, 1, 1, 1, 1, 113, 113, 113, 113, 113] 113
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37])
total number of confs: 183
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042535 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2NC(=O)C(=O)NC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 11, 11, 63, 113, 113, 113, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 113, 113, 113, 113, 1, 1, 1, 1, 1] 113
rigid atoms, others: [1, 34, 35, 36, 37, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 227
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042535 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042535
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042535/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042535
Building REAL300000042536
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042536'
/scratch/stefan/7769623/working/building/REAL300000042536 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042536

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042536/0 /scratch/stefan/7769623/working/building/REAL300000042536 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/589
`/scratch/stefan/7769623/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(F)C=CC=C1Cl)

`REAL300000042536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042536 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(F)C=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 63, 63, 63, 60, 63, 63, 63, 43, 43, 43, 10, 1, 1, 1, 1, 63, 62, 63] 63
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 125
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042536 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(F)C=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 38, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 63, 63, 63, 63, 1, 1, 1] 63
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 138
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042536 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042536
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042536/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042536
Building REAL300000042537
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042537'
/scratch/stefan/7769623/working/building/REAL300000042537 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042537

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042537/0 /scratch/stefan/7769623/working/building/REAL300000042537 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/590
`/scratch/stefan/7769623/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1OC)

`REAL300000042537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042537 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 40, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 12, 40, 67, 67, 67, 67, 2, 2, 2, 4, 4, 4] 82
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042537 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 67, 67, 67, 67, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 67, 67, 82, 82, 82, 82, 67, 67, 35, 9, 1, 1, 1, 1, 67, 67, 67, 82, 82, 82] 82
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042537 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042537
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042537/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042537
Building REAL300000042538
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042538'
/scratch/stefan/7769623/working/building/REAL300000042538 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042538

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042538/0 /scratch/stefan/7769623/working/building/REAL300000042538 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/591
`/scratch/stefan/7769623/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CSC=C2C(F)(F)F)=C1)

`REAL300000042538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042538 none O=C([O-])C1=CC=CC(NN=CC2=CSC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 13, 47, 47, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 13, 47, 70, 70, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 116
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042538 none O=C([O-])C1=CC=CC(NN=CC2=CSC=C2C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 70, 70, 70, 70, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 70, 70, 70, 70, 45, 8, 1, 1, 70] 70
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042538 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042538
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042538/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042538
Building REAL300000042539
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042539'
/scratch/stefan/7769623/working/building/REAL300000042539 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042539

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042539/0 /scratch/stefan/7769623/working/building/REAL300000042539 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/592
`/scratch/stefan/7769623/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CCN1C(=O)C(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21)

`REAL300000042539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042539 none C[NH+](C)CCN1C(=O)C(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 1, 1, 1, 1] 11
rigid atoms, others: [43, 5, 6, 7, 8, 9, 10, 11, 44, 45, 21, 22, 23, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 36
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042539 none C[NH+](C)CCN1C(=O)C(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 7, 7, 7, 7] 11
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 43
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042539 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042539
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042539/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042539
Building REAL300000042540
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042540'
/scratch/stefan/7769623/working/building/REAL300000042540 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042540

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042540/0 /scratch/stefan/7769623/working/building/REAL300000042540 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/593
`/scratch/stefan/7769623/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(S1)N(C)N=C2C)

`REAL300000042540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042540 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(S1)N(C)N=C2C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 8, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 74, 74, 74, 74, 74, 75, 74, 74, 74, 41, 41, 41, 10, 1, 1, 1, 1, 74, 75, 75, 75, 75, 75, 75] 75
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 127
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042540 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(S1)N(C)N=C2C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 8, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 56, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 55, 75, 75, 75, 74, 1, 2, 2, 2, 2, 2, 2] 75
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 183
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042540 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042540
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042540/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042540
Building REAL300000042541
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042541'
/scratch/stefan/7769623/working/building/REAL300000042541 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042541

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042541/0 /scratch/stefan/7769623/working/building/REAL300000042541 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/594
`/scratch/stefan/7769623/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CC2CCCO2)C2=CC=C(F)C=C2)=C1)

`REAL300000042541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042541 none O=C([O-])C1=CC=CC(NN=C(CC2CCCO2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 36, 107, 135, 135, 135, 135, 37, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 9, 107, 107, 135, 135, 135, 135, 135, 135, 135, 100, 100, 100, 100, 1] 144
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 549
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: REAL300000042541 none O=C([O-])C1=CC=CC(NN=C(CC2CCCO2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 40, 7, 7, 1, 7, 31, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 40, 31, 31, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 100] 144
rigid atoms, others: [38, 39, 40, 41, 10, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 366
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042541 none O=C([O-])C1=CC=CC(NN=C(CC2CCCO2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 135, 135, 135, 135, 79, 30, 30, 9, 1, 1, 1, 1, 1, 1, 30, 59, 59, 59, 59, 59, 59, 135, 135, 135, 135, 79, 9, 9, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 135] 144
rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42])
total number of confs: 347
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042541 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042541
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042541/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042541
Building REAL300000042542
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042542'
/scratch/stefan/7769623/working/building/REAL300000042542 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042542

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042542/0 /scratch/stefan/7769623/working/building/REAL300000042542 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/595
`/scratch/stefan/7769623/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(=O)N(C)C(=O)N1C)

`REAL300000042542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042542 none CN(C)C1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(=O)N(C)C(=O)N1C NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 11, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 12, 12, 68, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 68, 104, 104, 104, 104, 2, 2, 2, 2, 2, 2] 104
rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 237
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042542 none CN(C)C1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(=O)N(C)C(=O)N1C NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 11, 8, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 104, 104, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 60, 12, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104] 104
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 153
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042542 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042542
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042542/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042542
Building REAL300000042543
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042543'
/scratch/stefan/7769623/working/building/REAL300000042543 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042543

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042543/0 /scratch/stefan/7769623/working/building/REAL300000042543 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/596
`/scratch/stefan/7769623/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC=N1)

`REAL300000042543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042543 none CC(C)(C)CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 147, 144, 150, 141, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 147, 147, 147, 147, 150, 150, 150, 150, 150, 150, 150, 150, 150, 147, 147, 147, 147, 55, 1, 1, 1, 1, 147, 147] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 17, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 779
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042543 none CC(C)(C)CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 55, 59, 46, 11, 1, 11, 64, 64, 147, 147, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 50, 50, 50, 50, 11, 147, 147, 147, 147, 1, 1] 201
rigid atoms, others: [6, 41, 42, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 467
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042543 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042543/1 /scratch/stefan/7769623/working/building/REAL300000042543 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/597
`/scratch/stefan/7769623/working/3D/597' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC=N1)

`REAL300000042543.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042543/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042543 none CC(C)(C)CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 181, 183, 183, 181, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 96, 96, 96, 96, 183, 183, 183, 183, 183, 183, 183, 183, 183, 181, 181, 181, 181, 9, 1, 1, 1, 1, 96, 96] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 17, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 682
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042543 none CC(C)(C)CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 70, 76, 76, 70, 10, 1, 10, 10, 42, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 76, 70, 70, 70, 70, 42, 96, 96, 96, 96, 1, 1] 201
rigid atoms, others: [6, 41, 42, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 423
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042543 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042543
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042543/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042543/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042543
Building REAL300000042544
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042544'
/scratch/stefan/7769623/working/building/REAL300000042544 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042544

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042544/0 /scratch/stefan/7769623/working/building/REAL300000042544 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/598
`/scratch/stefan/7769623/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC(Cl)=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042544 none CN(C)C1=CC(Cl)=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 1, 1, 7, 19, 25, 25, 25, 25] 25
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042544 none CN(C)C1=CC(Cl)=CC(Cl)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 23, 25, 25, 25, 25, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 25, 25, 25, 25, 25, 16, 6, 1, 1, 1, 1] 25
rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 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
/scratch/stefan/7769623/working/building/REAL300000042544 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042544
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042544/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042544
Building REAL300000042545
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042545'
/scratch/stefan/7769623/working/building/REAL300000042545 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042545

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042545/0 /scratch/stefan/7769623/working/building/REAL300000042545 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/599
`/scratch/stefan/7769623/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OCC1=CC=CC=C1)C(N=NC1=CC=CC(C(=O)[O-])=C1)C(F)(F)F)

`REAL300000042545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042545 none CC(OCC1=CC=CC=C1)C(N=NC1=CC=CC(C(=O)[O-])=C1)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 13, 3, 1, 1, 1, 1, 1, 1, 1, 27, 65, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 65, 65, 27, 27, 27, 27, 3, 3, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41])
total number of confs: 466
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042545 none CC(OCC1=CC=CC=C1)C(N=NC1=CC=CC(C(=O)[O-])=C1)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 40, 89, 115, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 40, 40, 89, 89, 89, 89, 201, 201, 201, 201, 201, 201, 201, 40, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 815
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042545 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042545
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042545/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042545
Building REAL300000042546
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042546'
/scratch/stefan/7769623/working/building/REAL300000042546 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042546

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042546/0 /scratch/stefan/7769623/working/building/REAL300000042546 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/600
`/scratch/stefan/7769623/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=NN1C1=CC=CC=C1)

`REAL300000042546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042546 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 144, 144, 144, 144, 144, 146, 146, 144, 146, 146, 52, 52, 52, 12, 1, 1, 1, 1, 144, 146, 146, 146, 146, 146] 146
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042546 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [29, 6, 29, 29, 83, 146, 146, 146, 146, 146, 146, 146, 146, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 83, 146, 146, 146, 146, 6, 1, 1, 1, 1, 1] 146
rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 308
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042546 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 61, 144, 144, 144, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 12, 12, 12, 61, 144, 144, 144, 144, 1, 6, 6, 2, 6, 6] 146
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042546 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042546
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042546/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042546
Building REAL300000042547
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042547'
/scratch/stefan/7769623/working/building/REAL300000042547 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042547

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042547/0 /scratch/stefan/7769623/working/building/REAL300000042547 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/601
`/scratch/stefan/7769623/working/3D/601' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1)

`REAL300000042547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042547 none CCSCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 142, 86, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 98, 98, 38, 98, 98, 172, 172, 172, 172, 172, 86, 86, 6, 1, 1, 1, 1, 98, 98, 34, 98, 98] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 760
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042547 none CCSCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [117, 72, 27, 6, 1, 6, 6, 42, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 27, 27, 42, 98, 98, 98, 98, 1, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 4, 37, 38, 16, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 562
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042547 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042547
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042547/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042547
Building REAL300000042548
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042548'
/scratch/stefan/7769623/working/building/REAL300000042548 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042548

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042548/0 /scratch/stefan/7769623/working/building/REAL300000042548 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/602
`/scratch/stefan/7769623/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCNC(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042548 none CC(CCCCNC(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 5, 20, 37, 38, 39, 61, 148, 195, 195, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 38, 38, 38, 38, 40, 40, 60, 61, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [48, 49, 50, 47, 16, 17, 18, 19, 20, 21, 24, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 726
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042548 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042548
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042548/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042548
Building REAL300000042549
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042549'
/scratch/stefan/7769623/working/building/REAL300000042549 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042549

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042549/0 /scratch/stefan/7769623/working/building/REAL300000042549 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/603
`/scratch/stefan/7769623/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2Br)=C1)

`REAL300000042549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042549 none O=C([O-])C1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 33, 33, 57, 57, 57, 57, 57, 57, 33, 57, 57, 57, 1, 1, 1, 1, 13, 33, 57, 41, 57, 1] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042549 none O=C([O-])C1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 57, 57, 41, 10, 10, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 57, 57, 57, 57, 41, 10, 1, 1, 1, 57] 57
rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042549 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042549
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042549/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042549
Building REAL300000042550
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042550'
/scratch/stefan/7769623/working/building/REAL300000042550 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042550

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042550/0 /scratch/stefan/7769623/working/building/REAL300000042550 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/604
`/scratch/stefan/7769623/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)CCC2=C1F)

`REAL300000042550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042550 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)CCC2=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 6, 28, 28, 28, 28, 1, 1, 1, 1] 28
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 18, 19, 20, 21, 22, 36, 26, 27, 35] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 43
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042550 none COC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)CCC2=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 28, 28, 28, 28] 28
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 49
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042550 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042550
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042550/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042550
Building REAL300000042551
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042551'
/scratch/stefan/7769623/working/building/REAL300000042551 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042551

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042551/0 /scratch/stefan/7769623/working/building/REAL300000042551 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/605
`/scratch/stefan/7769623/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])=C1)

`REAL300000042551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042551 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 1, 1, 1, 1, 13, 50, 50, 62, 62, 62, 50, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 13, 50, 62, 50, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042551 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Cl)=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 62, 62, 62, 62, 34, 6, 1, 1, 62] 62
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042551 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042551
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042551/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042551
Building REAL300000042552
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042552'
/scratch/stefan/7769623/working/building/REAL300000042552 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042552

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042552/0 /scratch/stefan/7769623/working/building/REAL300000042552 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/606
`/scratch/stefan/7769623/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN3C=CC(Br)=CC3=N2)=C1)

`REAL300000042552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042552 none O=C([O-])C1=CC=CC(N=NCC2=CN3C=CC(Br)=CC3=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 1, 1, 47, 46, 99, 99, 99, 99, 1] 99
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042552 none O=C([O-])C1=CC=CC(N=NCC2=CN3C=CC(Br)=CC3=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 99, 99, 99, 99, 99, 99, 68, 68, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 9, 9, 1, 1, 1, 1, 99] 99
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042552 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042552/1 /scratch/stefan/7769623/working/building/REAL300000042552 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/607
`/scratch/stefan/7769623/working/3D/607' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN3C=CC(Br)=CC3=N2)=C1)

`REAL300000042552.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042552/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042552 none O=C([O-])C1=CC=CC(NN=CC2=CN3C=CC(Br)=CC3=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 11, 35, 35, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 11, 35, 38, 38, 38, 38, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042552 none O=C([O-])C1=CC=CC(NN=CC2=CN3C=CC(Br)=CC3=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 37, 38, 38, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 37, 38, 38, 22, 6, 1, 1, 1, 1, 38] 38
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042552 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042552
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042552/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042552/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042552
Building REAL300000042553
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042553'
/scratch/stefan/7769623/working/building/REAL300000042553 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042553

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042553/0 /scratch/stefan/7769623/working/building/REAL300000042553 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/608
`/scratch/stefan/7769623/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CN(C(=O)OC(C)(C)C)CCC1CN=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042553 none CC1CN(C(=O)OC(C)(C)C)CCC1CN=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 13, 14, 14, 14, 1, 1, 1, 1, 8, 49, 49, 101, 101, 101, 101, 101, 101, 101, 101, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 8, 8, 101, 101, 101, 101] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 11, 12, 13, 14, 44, 43, 45, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49, 50, 51])
total number of confs: 210
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042553 none CC1CN(C(=O)OC(C)(C)C)CCC1CN=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 101, 146, 146, 201, 201, 201, 201, 101, 101, 47, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 101, 101, 101, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 101, 101, 47, 47, 1, 1, 1, 1] 201
rigid atoms, others: [48, 51, 49, 50, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 574
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042553 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042553
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042553/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042553
Building REAL300000042554
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042554'
/scratch/stefan/7769623/working/building/REAL300000042554 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042554

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042554/0 /scratch/stefan/7769623/working/building/REAL300000042554 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/609
`/scratch/stefan/7769623/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1)

`REAL300000042554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042554 none O=C([O-])C1=CC=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 118, 148, 196, 201, 201, 196, 201, 201, 21, 42, 42, 33, 42, 42, 42, 1, 1, 1, 1, 5, 118, 118, 167, 167, 196, 196, 201, 201, 201, 201, 201, 42, 42, 42, 42, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 47, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1051
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042554 none O=C([O-])C1=CC=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 18, 4, 4, 1, 4, 30, 43, 77, 90, 90, 82, 90, 90, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 18, 30, 30, 52, 52, 77, 77, 90, 90, 90, 90, 90, 1, 1, 1, 1, 42] 201
rigid atoms, others: [10, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47])
total number of confs: 540
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042554 none O=C([O-])C1=CC=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=C(F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 145, 49, 49, 9, 5, 3, 1, 1, 1, 1, 1, 1, 1, 49, 90, 90, 72, 90, 90, 90, 201, 201, 201, 201, 145, 9, 9, 5, 5, 3, 3, 1, 1, 1, 1, 1, 90, 90, 90, 90, 201] 201
rigid atoms, others: [38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47])
total number of confs: 644
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042554 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042554
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042554/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042554
Building REAL300000042555
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042555'
/scratch/stefan/7769623/working/building/REAL300000042555 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042555

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042555/0 /scratch/stefan/7769623/working/building/REAL300000042555 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/610
`/scratch/stefan/7769623/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042555 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 54, 77, 77, 77, 77, 77, 78, 78, 77, 1, 1, 3, 3, 1, 1, 10, 54, 77, 77, 77, 77, 1, 1] 122
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 20, 21, 24, 25, 33] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 174
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042555 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 78, 122, 122, 78, 78, 77, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 78, 122, 122, 78, 77, 42, 12, 1, 1, 1, 1, 78, 78] 122
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 404
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042555 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042555
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042555/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042555
Building REAL300000042556
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042556'
/scratch/stefan/7769623/working/building/REAL300000042556 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042556

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042556/0 /scratch/stefan/7769623/working/building/REAL300000042556 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/611
`/scratch/stefan/7769623/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C(C)NC(=O)OC(C)(C)C)

`REAL300000042556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042556 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C(C)NC(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 76, 87, 135, 173, 173, 201, 201, 201, 201, 37, 37, 37, 37, 1, 1, 1, 1, 87, 87, 87, 87, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 777
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042556 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042556
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042556/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042556
Building REAL300000042557
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042557'
/scratch/stefan/7769623/working/building/REAL300000042557 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042557

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042557/0 /scratch/stefan/7769623/working/building/REAL300000042557 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/612
`/scratch/stefan/7769623/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1N1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1)

`REAL300000042557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042557 none CC1=CC=CC=C1N1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 49, 53, 53, 53, 53, 53, 53, 53, 53, 8, 8, 2, 2, 2, 1, 1, 1, 1, 8, 18, 49, 53, 53, 53, 53] 53
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30] set([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])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042557 none CC1=CC=CC=C1N1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 45, 53, 53, 45, 45, 45, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 53, 53, 53, 53, 45, 53, 53, 45, 28, 6, 1, 1, 1, 1] 53
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 106
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042557 none CC1=CC=CC=C1N1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 1, 8, 8, 1, 1, 1, 1, 1, 4, 4, 24, 45, 45, 45, 45, 45, 46, 46, 45, 1, 1, 8, 8, 8, 8, 1, 8, 8, 1, 4, 24, 45, 45, 45, 45] 53
rigid atoms, others: [6, 7, 8, 9, 10, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042557 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042557/1 /scratch/stefan/7769623/working/building/REAL300000042557 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/613
`/scratch/stefan/7769623/working/3D/613' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1N1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1)

`REAL300000042557.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042557/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042557 none CC1=CC=CC=C1N1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 39, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 2, 2, 2, 1, 1, 1, 1, 8, 39, 39, 201, 201, 201, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30] set([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])
total number of confs: 363
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042557 none CC1=CC=CC=C1N1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 201, 201, 146, 146, 146, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 146, 146, 201, 201, 201, 201, 182, 201, 201, 146, 46, 46, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 583
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042557 none CC1=CC=CC=C1N1C=C(CN=NC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 1, 8, 8, 1, 1, 1, 1, 1, 9, 65, 65, 146, 146, 146, 146, 146, 146, 146, 146, 1, 1, 8, 8, 8, 8, 3, 8, 8, 1, 9, 9, 146, 146, 146, 146] 201
rigid atoms, others: [6, 7, 8, 9, 10, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042557 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042557
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042557/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042557/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042557
Building REAL300000042558
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042558'
/scratch/stefan/7769623/working/building/REAL300000042558 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042558

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042558/0 /scratch/stefan/7769623/working/building/REAL300000042558 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/614
`/scratch/stefan/7769623/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C([N+](=O)[O-])C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042558 none COC(=O)C1=CC=C([N+](=O)[O-])C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [12, 13, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 33, 61, 61, 61, 61, 61, 61, 61, 61, 1, 13, 13, 13, 1, 1, 7, 33, 61, 61, 61, 61, 1] 101
rigid atoms, others: [2, 4, 5, 6, 7, 8, 11, 12, 24, 36, 28, 29] set([0, 1, 3, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 156
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042558 none COC(=O)C1=CC=C([N+](=O)[O-])C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 61, 101, 61, 61, 61, 61, 61, 61, 61, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 101, 101, 101, 61, 61, 31, 7, 1, 1, 1, 1, 61] 101
rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 239
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042558 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042558
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042558/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042558
Building REAL300000042559
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042559'
/scratch/stefan/7769623/working/building/REAL300000042559 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042559

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042559/0 /scratch/stefan/7769623/working/building/REAL300000042559 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/615
`/scratch/stefan/7769623/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042559 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 10, 10, 50, 73, 73, 73, 73, 73, 73, 73, 72, 1, 1, 1, 4, 4, 1, 1, 10, 50, 72, 73, 73, 72, 1] 83
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 20, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042559 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 72, 83, 83, 72, 72, 72, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 72, 72, 73, 83, 83, 72, 72, 42, 12, 1, 1, 1, 1, 72] 83
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 184
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042559 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042559
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042559/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042559
Building REAL300000042560
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042560'
/scratch/stefan/7769623/working/building/REAL300000042560 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042560

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042560/0 /scratch/stefan/7769623/working/building/REAL300000042560 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/616
`/scratch/stefan/7769623/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2[C@@H]3CCC[C@H]2CC2=CC=CC=C2C3)=C1)

`REAL300000042560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042560 none O=C([O-])C1=CC=CC(N=NC2[C@@H]3CCC[C@H]2CC2=CC=CC=C2C3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 26
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042560 none O=C([O-])C1=CC=CC(N=NC2[C@@H]3CCC[C@H]2CC2=CC=CC=C2C3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 7, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12] 12
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 26, 27, 28, 29])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042560 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042560
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042560/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042560
Building REAL300000042561
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042561'
/scratch/stefan/7769623/working/building/REAL300000042561 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042561

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042561/0 /scratch/stefan/7769623/working/building/REAL300000042561 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/617
`/scratch/stefan/7769623/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=C(F)C=CC=C2F)C=C1)

`REAL300000042561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042561 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 87, 87, 76, 87, 101, 101, 101, 87, 101, 101, 101, 87, 87, 49, 49, 49, 10, 1, 1, 1, 1, 87, 87, 101, 87, 101, 87, 87] 101
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 273
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: REAL300000042561 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [25, 3, 24, 25, 64, 101, 101, 101, 101, 101, 101, 101, 101, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 21, 25, 25, 64, 101, 101, 101, 101, 10, 10, 1, 1, 1, 10, 10] 101
rigid atoms, others: [37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41])
total number of confs: 248
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042561 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=C(F)C=CC=C2F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 30, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 1, 1, 6, 6, 6, 30, 87, 87, 87, 87, 1, 1, 6, 1, 6, 1, 1] 101
rigid atoms, others: [1, 35, 36, 40, 41, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39])
total number of confs: 163
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042561 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042561
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042561/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042561
Building REAL300000042562
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042562'
/scratch/stefan/7769623/working/building/REAL300000042562 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042562

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042562/0 /scratch/stefan/7769623/working/building/REAL300000042562 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/618
`/scratch/stefan/7769623/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CC=C2NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1)

`REAL300000042562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042562 none CC(C)(C)C1=CC=C2NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 165, 165, 165, 165, 165, 165, 165, 164, 1, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 1, 1, 1, 1, 9, 60, 165, 165, 165, 164, 1] 165
rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 44, 23, 24, 36, 37] set([0, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43])
total number of confs: 304
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042562 none CC(C)(C)C1=CC=C2NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [165, 165, 165, 165, 165, 165, 165, 164, 164, 164, 69, 69, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 164, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 164, 164, 164, 69, 12, 1, 1, 1, 1, 165] 165
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042562 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042562
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042562/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042562
Building REAL300000042563
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042563'
/scratch/stefan/7769623/working/building/REAL300000042563 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042563

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042563/0 /scratch/stefan/7769623/working/building/REAL300000042563 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/619
`/scratch/stefan/7769623/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042563 none CC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 42, 55, 55, 55, 55, 55, 55, 55, 55, 1, 2, 2, 2, 1, 11, 42, 55, 55, 55, 55] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042563 none CC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 55, 36, 36, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 55, 55, 55, 36, 12, 1, 1, 1, 1] 55
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042563 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042563
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042563/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042563
Building REAL300000042564
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042564'
/scratch/stefan/7769623/working/building/REAL300000042564 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042564

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042564/0 /scratch/stefan/7769623/working/building/REAL300000042564 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/620
`/scratch/stefan/7769623/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC(Cl)=C3)C2)=C1)

`REAL300000042564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042564 none O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 34, 34, 34, 34, 104, 104, 104, 104, 104, 104, 34, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 104, 104, 104, 104, 34, 34, 1] 104
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042564 none O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 59, 59, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 104, 104, 104, 104, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 104] 104
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 167
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042564 none O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 34, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 34] 104
rigid atoms, others: [32, 33, 34, 39, 40, 9, 10, 11, 12, 13, 14, 15, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 35, 36, 37, 38, 41])
total number of confs: 54
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042564 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042564
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042564/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042564
Building REAL300000042565
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042565'
/scratch/stefan/7769623/working/building/REAL300000042565 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042565

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042565/0 /scratch/stefan/7769623/working/building/REAL300000042565 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/621
`/scratch/stefan/7769623/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC(C1=CC=CC=C1F)C(C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042565 none CC(=O)NC(C1=CC=CC=C1F)C(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 77, 77, 129, 129, 129, 129, 129, 129, 129, 129, 11, 11, 11, 11, 7, 1, 1, 1, 1, 20, 20, 20, 20, 129, 129, 129, 129] 132
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 254
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042565 none CC(=O)NC(C1=CC=CC=C1F)C(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [105, 105, 105, 87, 39, 87, 129, 129, 114, 129, 129, 129, 8, 39, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 105, 105, 105, 105, 87, 129, 129, 129, 129, 39, 39, 39, 39, 1, 1, 1, 1] 132
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 545
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042565 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042565
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042565/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042565
Building REAL300000042566
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042566'
/scratch/stefan/7769623/working/building/REAL300000042566 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042566

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042566/0 /scratch/stefan/7769623/working/building/REAL300000042566 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/622
`/scratch/stefan/7769623/working/3D/622' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1)

`REAL300000042566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 10, 10, 3, 3, 3, 3, 3, 3, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 3, 3, 14] 14
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 30
number of broken/clashed sets: 3
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 14, 14, 13, 13, 14, 14, 13, 14, 14, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 13, 14, 14, 14, 14, 14, 13, 13, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 48, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 34
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: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 11, 11, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 5, 5, 4, 5, 5, 4, 14, 14, 14, 14, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 5, 5, 5, 5, 5, 4, 4, 14] 14
rigid atoms, others: [35, 36, 37, 38, 39, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 31
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 3, 3, 1, 3, 3, 1, 13, 13, 13, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 3, 3, 3, 3, 3, 1, 1, 13] 14
rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 14, 15, 18, 19, 46, 25, 47, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 48])
total number of confs: 34
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042566 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042566/1 /scratch/stefan/7769623/working/building/REAL300000042566 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/623
`/scratch/stefan/7769623/working/3D/623' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1)

`REAL300000042566.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042566/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 11] 11
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 17
number of broken/clashed sets: 11
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 48, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 16
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: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 7, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11] 11
rigid atoms, others: [35, 36, 37, 38, 39, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 17
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042566 none O=C([O-])C1=CC=CC(N=NC2CC[N@@H+](C3CC3)C(C3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 1, 1, 11] 11
rigid atoms, others: [32, 33, 34, 40, 9, 10, 11, 12, 13, 14, 15, 18, 19, 46, 25, 47, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 48])
total number of confs: 23
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042566 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042566
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042566/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042566/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042566
Building REAL300000042567
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042567'
/scratch/stefan/7769623/working/building/REAL300000042567 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042567

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042567/0 /scratch/stefan/7769623/working/building/REAL300000042567 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/624
`/scratch/stefan/7769623/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(Br)C=C32)=CC=C1)

`REAL300000042567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042567 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(Br)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 7, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042567 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(Br)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 9, 9, 9] 9
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042567 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042567/1 /scratch/stefan/7769623/working/building/REAL300000042567 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/625
`/scratch/stefan/7769623/working/3D/625' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(Br)C=C32)=CC=C1)

`REAL300000042567.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042567/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042567 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(Br)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 1, 1, 1, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [2, 1, 2, 1, 1, 1, 1, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 12, 19, 19, 38, 19, 1, 1, 1] 40
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042567 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(Br)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 17, 1, 1, 1, 1, 1, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [20, 19, 20, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 7, 1, 1, 2, 1, 19, 19, 19] 40
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 28] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 27, 29, 30, 31])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042567 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042567
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042567/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042567/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042567
Building REAL300000042568
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042568'
/scratch/stefan/7769623/working/building/REAL300000042568 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042568

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042568/0 /scratch/stefan/7769623/working/building/REAL300000042568 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/626
`/scratch/stefan/7769623/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=CC=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042568 none CC(C)C1=CC=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 24, 25, 25, 24, 3, 3, 3, 2, 3, 3, 3, 1, 1, 1, 1, 5, 24, 24, 24, 24] 25
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 33, 31] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39])
total number of confs: 57
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042568 none CC(C)C1=CC=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 24, 25, 25, 25, 24, 24, 24, 24, 10, 1, 1, 1, 1] 25
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042568 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042568
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042568/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042568
Building REAL300000042569
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042569'
/scratch/stefan/7769623/working/building/REAL300000042569 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042569

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042569/0 /scratch/stefan/7769623/working/building/REAL300000042569 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/627
`/scratch/stefan/7769623/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)OC(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042569 none COC1=CC=C2C(=C1)OC(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 9, 43, 43, 43, 43] 43
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 35, 36, 37, 38] set([0, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 39, 40, 41, 42, 43])
total number of confs: 77
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042569 none COC1=CC=C2C(=C1)OC(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 11, 1, 1, 1, 1] 43
rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 69
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042569 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042569
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042569/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042569
Building REAL300000042570
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042570'
/scratch/stefan/7769623/working/building/REAL300000042570 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042570

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042570/0 /scratch/stefan/7769623/working/building/REAL300000042570 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/628
`/scratch/stefan/7769623/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1)

`REAL300000042570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042570 none CC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 12, 12, 55, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 2, 2, 2, 1, 12, 55, 72, 72, 72, 72, 1] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042570 none CC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 72, 72, 72, 72, 72, 72, 72, 44, 10, 1, 1, 1, 1, 72] 72
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042570 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042570
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042570/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042570
Building REAL300000042571
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042571'
/scratch/stefan/7769623/working/building/REAL300000042571 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042571

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042571/0 /scratch/stefan/7769623/working/building/REAL300000042571 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/629
`/scratch/stefan/7769623/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CN=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042571 none COC(=O)C1=CN=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 76, 76, 151, 151, 151, 151, 151, 151, 151, 151, 1, 8, 8, 8, 1, 13, 13, 13, 13, 151, 151, 151, 151] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 21, 25] set([0, 1, 3, 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: 259
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042571 none COC(=O)C1=CN=C(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 201, 151, 151, 151, 52, 8, 52, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 151, 201, 201, 201, 151, 52, 52, 52, 52, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 492
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042571 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042571
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042571/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042571
Building REAL300000042572
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042572'
/scratch/stefan/7769623/working/building/REAL300000042572 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042572

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042572/0 /scratch/stefan/7769623/working/building/REAL300000042572 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/630
`/scratch/stefan/7769623/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(O)=C2Br)=C1)

`REAL300000042572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042572 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(O)=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 32, 32, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 11, 32, 40, 40, 40, 80, 1] 80
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28])
total number of confs: 148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042572 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(O)=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [40, 40, 40, 40, 40, 40, 40, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 32, 9, 1, 1, 1, 2, 40] 80
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28, 29])
total number of confs: 90
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042572 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042572/1 /scratch/stefan/7769623/working/building/REAL300000042572 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/631
`/scratch/stefan/7769623/working/3D/631' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC([O-])=C2Br)=C1)

`REAL300000042572.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042572/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042572 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC([O-])=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 26
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042572 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC([O-])=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 12, 6, 1, 1, 1, 15] 15
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042572 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042572
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042572/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042572/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042572
Building REAL300000042573
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042573'
/scratch/stefan/7769623/working/building/REAL300000042573 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042573

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042573/0 /scratch/stefan/7769623/working/building/REAL300000042573 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/632
`/scratch/stefan/7769623/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1)

`REAL300000042573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042573 none CC(C)(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 39, 39, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 36, 36, 26, 28, 36, 36, 39, 39, 39, 39, 39, 39, 39, 39, 39, 35, 35, 8, 1, 1, 1, 1, 36, 36, 36, 36] 39
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 16, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43])
total number of confs: 169
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042573 none CC(C)(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 7, 14, 14, 6, 1, 6, 6, 20, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 20, 36, 36, 36, 36, 1, 1, 1, 1] 39
rigid atoms, others: [5, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 119
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042573 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042573
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042573/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042573
Building REAL300000042574
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042574'
/scratch/stefan/7769623/working/building/REAL300000042574 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042574

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042574/0 /scratch/stefan/7769623/working/building/REAL300000042574 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/633
`/scratch/stefan/7769623/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=CC(Cl)=C3)C2)=C1)

`REAL300000042574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042574 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 17, 17, 49, 49, 49, 49, 49, 49, 17, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 49, 49, 49, 49, 17, 17, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 81
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: REAL300000042574 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 28, 28, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 49, 49, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 49] 49
rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 82
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042574 none O=C([O-])C1=CC=CC(N=NC2CCC(C3=CC=CC(Cl)=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 1, 1, 17] 49
rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 21, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 32, 33, 34, 35, 38])
total number of confs: 33
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042574 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042574
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042574/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042574
Building REAL300000042575
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042575'
/scratch/stefan/7769623/working/building/REAL300000042575 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042575

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042575/0 /scratch/stefan/7769623/working/building/REAL300000042575 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/634
`/scratch/stefan/7769623/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042575 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [5, 1, 5, 5, 1, 1, 1, 1, 1, 10, 10, 51, 82, 82, 82, 82, 82, 83, 83, 82, 1, 5, 5, 1, 1, 10, 51, 82, 82, 82, 82] 161
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 23, 24] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042575 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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, 82, 161, 161, 82, 82, 82, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 161, 161, 82, 82, 54, 12, 1, 1, 1, 1] 161
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 493
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042575 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042575
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042575/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042575
Building REAL300000042576
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042576'
/scratch/stefan/7769623/working/building/REAL300000042576 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042576

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042576/0 /scratch/stefan/7769623/working/building/REAL300000042576 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/635
`/scratch/stefan/7769623/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=CC(O)=C3F)=CC=C1)

`REAL300000042576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042576 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=CC(O)=C3F)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 1, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 11, 17, 17, 17, 34, 1, 1, 1] 36
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042576 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=CC(O)=C3F)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 1, 7, 6, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [18, 17, 18, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 7, 1, 1, 1, 2, 17, 17, 17] 36
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 36
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042576 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042576/1 /scratch/stefan/7769623/working/building/REAL300000042576 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/636
`/scratch/stefan/7769623/working/3D/636' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=CC([O-])=C3F)=CC=C1)

`REAL300000042576.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042576/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042576 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=CC([O-])=C3F)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 1, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 20
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042576 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=CC([O-])=C3F)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 12, 1, 15, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 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, 8, 9, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 1, 1, 8, 8, 8] 9
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042576 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042576
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042576/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042576/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042576
Building REAL300000042577
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042577'
/scratch/stefan/7769623/working/building/REAL300000042577 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042577

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042577/0 /scratch/stefan/7769623/working/building/REAL300000042577 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/637
`/scratch/stefan/7769623/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(OCC3=CC=CC=C3)C=C2)=C1)

`REAL300000042577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042577 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(OCC3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39, 116, 132, 132, 116, 116, 201, 201, 201, 201, 201, 201, 201, 132, 132, 1, 1, 1, 1, 38, 39, 116, 116, 132, 132, 201, 201, 201, 201, 201, 201, 201, 132, 132, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 46, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 620
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042577 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(OCC3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 152, 152, 58, 58, 16, 3, 3, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 58, 58, 16, 16, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6, 201] 201
rigid atoms, others: [39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 418
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042577 none O=C([O-])C1=CC=CC(N=NC=CCC2=CC=C(OCC3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [132, 132, 132, 132, 132, 132, 132, 63, 63, 15, 15, 3, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 132, 132, 132, 132, 15, 15, 3, 3, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 132] 201
rigid atoms, others: [45, 35, 36, 44, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 46])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042577 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042577
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042577/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042577
Building REAL300000042578
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042578'
/scratch/stefan/7769623/working/building/REAL300000042578 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042578

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042578/0 /scratch/stefan/7769623/working/building/REAL300000042578 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/638
`/scratch/stefan/7769623/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C2=CC=CC=C2C)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042578 none COC1=CC=C(C2=CC=CC=C2C)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 12, 12, 39, 81, 81, 81, 81, 81, 82, 82, 81, 4, 4, 4, 1, 1, 7, 7, 6, 7, 7, 7, 7, 1, 12, 39, 81, 81, 81, 81] 160
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 13, 14, 15, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042578 none COC1=CC=C(C2=CC=CC=C2C)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [107, 81, 81, 81, 81, 81, 81, 160, 160, 160, 160, 160, 160, 81, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 108, 108, 108, 81, 81, 160, 160, 160, 160, 160, 160, 160, 81, 35, 8, 1, 1, 1, 1] 160
rigid atoms, others: [42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 306
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042578 none COC1=CC=C(C2=CC=CC=C2C)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 112, 160, 160, 160, 160, 160, 160, 160, 160, 19, 19, 19, 7, 7, 1, 1, 1, 1, 2, 2, 2, 7, 39, 112, 160, 160, 160, 160] 160
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 368
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042578 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042578
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042578/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042578
Building REAL300000042579
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042579'
/scratch/stefan/7769623/working/building/REAL300000042579 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042579

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042579/0 /scratch/stefan/7769623/working/building/REAL300000042579 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/639
`/scratch/stefan/7769623/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042579 none CC1=CC=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 20, 20, 53, 63, 63, 63, 63, 63, 63, 63, 63, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 20, 53, 63, 63, 63, 63] 63
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042579 none CC1=CC=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 59, 63, 63, 44, 44, 44, 44, 44, 44, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 63, 63, 63, 63, 63, 63, 44, 44, 44, 44, 31, 7, 1, 1, 1, 1] 63
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 128
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042579 none CC1=CC=CC=C1C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 10, 32, 44, 44, 44, 44] 63
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 107
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042579 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042579
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042579/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042579
Building REAL300000042580
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042580'
/scratch/stefan/7769623/working/building/REAL300000042580 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042580

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042580/0 /scratch/stefan/7769623/working/building/REAL300000042580 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/640
`/scratch/stefan/7769623/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1)

`REAL300000042580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042580 none CC1=CC(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 1, 1, 1, 1, 12, 12, 46, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 2, 2, 2, 1, 2, 12, 46, 64, 64, 64, 64, 1] 128
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 153
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042580 none CC1=CC(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [64, 64, 64, 64, 64, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 64, 64, 64, 64, 64, 64, 64, 128, 36, 10, 1, 1, 1, 1, 64] 128
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 233
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042580 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042580
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042580/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042580
Building REAL300000042581
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042581'
/scratch/stefan/7769623/working/building/REAL300000042581 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042581

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042581/0 /scratch/stefan/7769623/working/building/REAL300000042581 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/641
`/scratch/stefan/7769623/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C2=CC=CC=C2)=NN1C)

`REAL300000042581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042581 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C2=CC=CC=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 166, 166, 166, 182, 182, 182, 182, 182, 166, 166, 166, 56, 56, 56, 10, 1, 1, 1, 1, 166, 182, 182, 182, 182, 182, 166, 166, 166] 182
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 272
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: REAL300000042581 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C2=CC=CC=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 7, 49, 49, 138, 182, 182, 182, 182, 182, 182, 182, 182, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 49, 49, 49, 138, 182, 182, 182, 182, 7, 1, 1, 1, 1, 1, 7, 7, 7] 182
rigid atoms, others: [34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 435
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042581 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C2=CC=CC=C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 57, 166, 166, 166, 166, 166, 166, 166, 166, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 1, 10, 10, 10, 57, 166, 166, 166, 166, 1, 7, 7, 2, 7, 7, 2, 2, 2] 182
rigid atoms, others: [1, 33, 13, 14, 15, 16, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 302
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042581 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042581
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042581/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042581
Building REAL300000042582
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042582'
/scratch/stefan/7769623/working/building/REAL300000042582 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042582

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042582/0 /scratch/stefan/7769623/working/building/REAL300000042582 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/642
`/scratch/stefan/7769623/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(F)C=C2)=N1)

`REAL300000042582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042582 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 11, 11, 65, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 6, 6, 1, 2, 6, 6, 1, 2, 2, 2, 1, 11, 65, 159, 159, 159, 159, 6, 6, 6, 6] 170
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 304
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: REAL300000042582 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 29, 29, 114, 170, 170, 170, 170, 170, 170, 170, 170, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 29, 114, 170, 170, 170, 170, 1, 1, 1, 1] 170
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 368
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042582 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [159, 159, 159, 74, 74, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 159, 159, 170, 170, 159, 170, 170, 170, 159, 159, 159, 159, 159, 74, 13, 1, 1, 1, 1, 170, 170, 170, 170] 170
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 15, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 306
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042582 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042582
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042582/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042582
Building REAL300000042583
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042583'
/scratch/stefan/7769623/working/building/REAL300000042583 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042583

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042583/0 /scratch/stefan/7769623/working/building/REAL300000042583 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/643
`/scratch/stefan/7769623/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC3=C2OC(F)(F)O3)=C1)

`REAL300000042583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042583 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC3=C2OC(F)(F)O3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 41, 41, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 9, 41, 54, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042583 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC3=C2OC(F)(F)O3)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 34, 9, 1, 1, 1, 54] 54
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042583 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042583
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042583/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042583
Building REAL300000042584
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042584'
/scratch/stefan/7769623/working/building/REAL300000042584 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042584

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042584/0 /scratch/stefan/7769623/working/building/REAL300000042584 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/644
`/scratch/stefan/7769623/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3F)C2)=C1)

`REAL300000042584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042584 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3F)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 46, 46, 46, 98, 98, 98, 98, 98, 98, 98, 46, 1, 1, 1, 1, 46, 46, 46, 46, 98, 98, 98, 46, 46, 1] 98
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 177
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: REAL300000042584 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3F)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 69, 69, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 98, 98, 98, 98, 10, 10, 10, 10, 1, 1, 1, 10, 10, 98] 98
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 140
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042584 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(Br)C=C3F)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 46, 46, 46, 46, 46, 13, 13, 1, 1, 1, 1, 1, 10, 10, 7, 9, 10, 10, 10, 1, 46, 46, 46, 46, 1, 1, 1, 1, 10, 10, 10, 1, 1, 46] 98
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 35])
total number of confs: 77
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042584 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042584
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042584/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042584
Building REAL300000042585
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042585'
/scratch/stefan/7769623/working/building/REAL300000042585 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042585

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042585/0 /scratch/stefan/7769623/working/building/REAL300000042585 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/645
`/scratch/stefan/7769623/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042585 none CS(=O)(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 67, 119, 119, 119, 119, 119, 119, 119, 119, 1, 3, 3, 3, 1, 1, 1, 13, 67, 119, 119, 119, 119, 1] 164
rigid atoms, others: [1, 34, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 252
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042585 none CS(=O)(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 119, 164, 164, 119, 61, 119, 119, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 119, 164, 164, 164, 61, 119, 119, 61, 12, 1, 1, 1, 1, 119] 164
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 590
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042585 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042585
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042585/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042585
Building REAL300000042586
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042586'
/scratch/stefan/7769623/working/building/REAL300000042586 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042586

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042586/0 /scratch/stefan/7769623/working/building/REAL300000042586 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/646
`/scratch/stefan/7769623/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042586 none CC(C)(C)OC(=O)CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 60, 64, 64, 45, 6, 45, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 52, 52, 52, 52, 52, 53, 53, 52, 64, 64, 64, 64, 64, 64, 64, 64, 64, 6, 6, 1, 1, 1, 8, 26, 52, 52, 52, 52] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042586 none CC(C)(C)OC(=O)CN1C=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 189, 88, 189, 52, 52, 52, 52, 52, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 88, 52, 52, 52, 20, 6, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 572
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042586 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042586
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042586/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042586
Building REAL300000042587
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042587'
/scratch/stefan/7769623/working/building/REAL300000042587 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042587

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042587/0 /scratch/stefan/7769623/working/building/REAL300000042587 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/647
`/scratch/stefan/7769623/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC3=CC=CC(Cl)=C3C2)=C1)

`REAL300000042587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042587 none O=C([O-])C1=CC=CC(N=NC2CCC3=CC=CC(Cl)=C3C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 28
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042587 none O=C([O-])C1=CC=CC(N=NC2CCC3=CC=CC(Cl)=C3C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24])
total number of confs: 20
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042587 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042587
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042587/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042587
Building REAL300000042588
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042588'
/scratch/stefan/7769623/working/building/REAL300000042588 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042588

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042588/0 /scratch/stefan/7769623/working/building/REAL300000042588 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/648
`/scratch/stefan/7769623/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042588 none CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 8, 8, 45, 63, 63, 63, 63, 63, 64, 64, 63, 2, 2, 2, 7, 7, 6, 7, 1, 8, 45, 63, 63, 63, 63] 112
rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042588 none CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 112, 112, 111, 112, 112, 112, 63, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 64, 64, 64, 112, 112, 111, 112, 63, 29, 8, 1, 1, 1, 1] 112
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 207
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042588 none CC1=NN(C2=CC=CC(F)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 35, 96, 111, 112, 111, 112, 112, 112, 112, 112, 7, 7, 7, 1, 1, 1, 1, 7, 35, 96, 112, 112, 112, 112] 112
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 276
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042588 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042588
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042588/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042588
Building REAL300000042589
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042589'
/scratch/stefan/7769623/working/building/REAL300000042589 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042589

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042589/0 /scratch/stefan/7769623/working/building/REAL300000042589 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/649
`/scratch/stefan/7769623/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1)

`REAL300000042589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042589 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 58, 58, 58, 59, 59, 59, 59, 59, 59, 58, 34, 34, 34, 10, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59] 59
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 105
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: REAL300000042589 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [20, 4, 20, 20, 44, 59, 59, 59, 59, 59, 59, 59, 59, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 20, 44, 59, 59, 59, 59, 4, 1, 1, 1, 1, 1] 59
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])
total number of confs: 135
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042589 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 30, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 10, 10, 10, 29, 59, 59, 59, 58, 1, 4, 4, 1, 4, 4] 59
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 128
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042589 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042589/1 /scratch/stefan/7769623/working/building/REAL300000042589 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/650
`/scratch/stefan/7769623/working/3D/650' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1)

`REAL300000042589.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042589/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042589 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 55, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042589 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 36, 160, 160, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 36, 36, 36, 36, 201, 201, 201, 201, 4, 1, 1, 1, 1, 1] 201
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])
total number of confs: 345
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042589 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 13, 13, 13, 13, 201, 201, 201, 201, 1, 4, 4, 1, 4, 4] 201
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 314
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042589 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042589
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042589/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042589/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042589
Building REAL300000042590
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042590'
/scratch/stefan/7769623/working/building/REAL300000042590 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042590

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042590/0 /scratch/stefan/7769623/working/building/REAL300000042590 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/651
`/scratch/stefan/7769623/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C3OCCCCOC3=C2)=C1)

`REAL300000042590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042590 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3OCCCCOC3=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 12, 45, 45, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 12, 45, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042590 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3OCCCCOC3=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 69, 70, 70, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 69, 70, 70, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70] 70
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 40, 23, 24, 25, 26, 27, 28])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042590 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042590
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042590/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042590
Building REAL300000042591
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042591'
/scratch/stefan/7769623/working/building/REAL300000042591 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042591

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042591/0 /scratch/stefan/7769623/working/building/REAL300000042591 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/652
`/scratch/stefan/7769623/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC(Br)=C2)=C1)

`REAL300000042591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042591 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 35, 35, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 13, 35, 68, 68, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042591 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 47, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 46, 10, 1, 1, 1, 68] 68
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042591 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042591
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042591/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042591
Building REAL300000042592
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042592'
/scratch/stefan/7769623/working/building/REAL300000042592 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042592

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042592/0 /scratch/stefan/7769623/working/building/REAL300000042592 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/653
`/scratch/stefan/7769623/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)COC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042592 none CC(C)COC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 28, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 78, 78, 78, 78, 78, 78, 78, 78, 43, 43, 43, 43, 43, 43, 43, 28, 28, 1, 1, 1, 1, 7, 30, 78, 78, 78, 78] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 366
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042592 none CC(C)COC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [197, 201, 201, 159, 78, 78, 78, 41, 78, 78, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 39, 8, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 661
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042592 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042592
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042592/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042592
Building REAL300000042593
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042593'
/scratch/stefan/7769623/working/building/REAL300000042593 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042593

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042593/0 /scratch/stefan/7769623/working/building/REAL300000042593 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/654
`/scratch/stefan/7769623/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(Br)=CS1)

`REAL300000042593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042593 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(Br)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 17, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 107, 107, 107, 107, 107, 43, 43, 43, 43, 1, 1, 1, 1, 107] 107
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042593 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NC(Br)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'C.2', 'Br', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 17, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [13, 1, 13, 73, 73, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 107, 107, 107, 107, 1] 107
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 175
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042593 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042593
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042593/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042593
Building REAL300000042594
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042594'
/scratch/stefan/7769623/working/building/REAL300000042594 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042594

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042594/0 /scratch/stefan/7769623/working/building/REAL300000042594 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/655
`/scratch/stefan/7769623/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OC(=O)CC)

`REAL300000042594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042594 none CCOC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OC(=O)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 11, 5, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 10, 1, 1, 1, 1, 1, 7, 7, 13, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 7, 26, 26, 95, 28, 28, 28, 28, 28, 1, 7, 13, 17, 17, 17, 17, 1, 1, 95, 95, 95, 95, 95] 201
rigid atoms, others: [2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 38, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 432
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042594 none CCOC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1OC(=O)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 11, 5, 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, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 67, 17, 17, 17, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 16, 16, 74, 127, 127, 186, 93, 93, 93, 93, 93, 17, 5, 3, 1, 1, 1, 1, 17, 17, 186, 186, 186, 186, 186] 201
rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 797
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042594 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042594
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042594/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042594
Building REAL300000042595
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042595'
/scratch/stefan/7769623/working/building/REAL300000042595 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042595

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042595/0 /scratch/stefan/7769623/working/building/REAL300000042595 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/656
`/scratch/stefan/7769623/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042595 none CS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 1, 1, 1, 1, 1, 8, 8, 54, 122, 122, 122, 122, 122, 123, 123, 122, 1, 7, 7, 7, 1, 1, 8, 54, 122, 122, 122, 122] 149
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042595 none CS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [149, 122, 149, 149, 122, 122, 122, 64, 64, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 122, 149, 149, 149, 122, 122, 64, 12, 1, 1, 1, 1] 149
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 347
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042595 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042595
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042595/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042595
Building REAL300000042596
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042596'
/scratch/stefan/7769623/working/building/REAL300000042596 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042596

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042596/0 /scratch/stefan/7769623/working/building/REAL300000042596 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/657
`/scratch/stefan/7769623/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1C(F)(F)F)

`REAL300000042596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042596 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 50, 70, 70, 70, 70, 70, 70, 70, 69, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 8, 50, 70, 70, 70, 69, 1, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 16, 17, 18, 19, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042596 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 69, 69, 69, 69, 70, 70, 70, 70, 70, 70, 69, 37, 10, 1, 1, 1, 1, 69, 69] 70
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 134
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042596 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042596
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042596/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042596
Building REAL300000042597
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042597'
/scratch/stefan/7769623/working/building/REAL300000042597 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042597

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042597/0 /scratch/stefan/7769623/working/building/REAL300000042597 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/658
`/scratch/stefan/7769623/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042597 none CS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 1, 1, 1, 1, 1, 8, 8, 46, 98, 98, 98, 98, 98, 99, 99, 98, 1, 7, 7, 7, 1, 1, 8, 46, 98, 98, 98, 98] 133
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 209
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042597 none CS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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, 98, 133, 133, 98, 98, 98, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 98, 133, 133, 133, 98, 98, 55, 12, 1, 1, 1, 1] 133
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 362
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042597 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042597
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042597/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042597
Building REAL300000042598
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042598'
/scratch/stefan/7769623/working/building/REAL300000042598 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042598

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042598/0 /scratch/stefan/7769623/working/building/REAL300000042598 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/659
`/scratch/stefan/7769623/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=CC=C2CCCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1)

`REAL300000042598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042598 none NC1=CC=C2CCCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 20, 20, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 1] 20
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40] set([35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042598 none NC1=CC=C2CCCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 19] 20
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 38
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042598 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042598
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042598/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042598
Building REAL300000042599
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042599'
/scratch/stefan/7769623/working/building/REAL300000042599 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042599

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042599/0 /scratch/stefan/7769623/working/building/REAL300000042599 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/660
`/scratch/stefan/7769623/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C=C2I)=C1)

`REAL300000042599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042599 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C=C2I)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 38, 38, 50, 50, 40, 40, 50, 50, 50, 1, 1, 1, 1, 13, 38, 50, 50, 50, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 109
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042599 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C=C2I)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 10, 1, 1, 1, 50] 50
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042599 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042599
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042599/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042599
Building REAL300000042600
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042600'
/scratch/stefan/7769623/working/building/REAL300000042600 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042600

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042600/0 /scratch/stefan/7769623/working/building/REAL300000042600 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/661
`/scratch/stefan/7769623/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(CC)C(=O)NCCC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042600 none CCC1(CC)C(=O)NCCC1N=NC1=CC=CC(C(=O)[O-])=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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 9
rigid atoms, others: [32, 1, 2, 3, 36, 5, 6, 7, 8, 9, 10, 11, 34, 35, 33, 37] set([0, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042600 none CCC1(CC)C(=O)NCCC1N=NC1=CC=CC(C(=O)[O-])=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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042600 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042600
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042600/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042600
Building REAL300000042601
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042601'
/scratch/stefan/7769623/working/building/REAL300000042601 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042601

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042601/0 /scratch/stefan/7769623/working/building/REAL300000042601 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/662
`/scratch/stefan/7769623/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1CC1=CC=CC=C1)

`REAL300000042601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042601 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 46, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 6, 12, 13, 8, 13, 12, 2, 2, 2, 1, 6, 45, 97, 97, 97, 97, 2, 2, 2, 6, 6, 12, 13, 13, 13, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 236
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: REAL300000042601 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 48, 48, 149, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 48, 150, 201, 201, 201, 201, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 493
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042601 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 97, 97, 97, 97, 156, 201, 201, 201, 201, 201, 97, 97, 97, 97, 41, 9, 1, 1, 1, 1, 97, 97, 97, 156, 156, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 568
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042601 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042601
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042601/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042601
Building REAL300000042602
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042602'
/scratch/stefan/7769623/working/building/REAL300000042602 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042602

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042602/0 /scratch/stefan/7769623/working/building/REAL300000042602 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/663
`/scratch/stefan/7769623/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C1(C)C)

`REAL300000042602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042602 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C1(C)C 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 44, 44, 13, 7, 13, 1, 1, 1, 1, 1, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 7, 1, 1, 1, 1, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 155
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042602 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C1(C)C 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 182, 136, 182, 48, 48, 48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 48, 48, 48, 48, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48] 201
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48])
total number of confs: 560
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042602 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042602
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042602/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042602
Building REAL300000042603
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042603'
/scratch/stefan/7769623/working/building/REAL300000042603 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042603

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042603/0 /scratch/stefan/7769623/working/building/REAL300000042603 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/664
`/scratch/stefan/7769623/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCO[C@@H]1CC(N=NC2=CC=CC(C(=O)[O-])=C2)[C@]12CCCO2)

`REAL300000042603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042603 none CCO[C@@H]1CC(N=NC2=CC=CC(C(=O)[O-])=C2)[C@]12CCCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 5, 7, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1] 44
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 40, 39, 18, 19, 20, 21, 22, 36, 38, 28, 29, 30, 37] set([0, 1, 34, 33, 32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 31])
total number of confs: 62
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042603 none CCO[C@@H]1CC(N=NC2=CC=CC(C(=O)[O-])=C2)[C@]12CCCO2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 12, 5, 7, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 31, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 31, 44, 44, 44, 44, 44, 31, 31, 31, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31] 44
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 101
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042603 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042603
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042603/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042603
Building REAL300000042604
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042604'
/scratch/stefan/7769623/working/building/REAL300000042604 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042604

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042604/0 /scratch/stefan/7769623/working/building/REAL300000042604 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/665
`/scratch/stefan/7769623/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1O)

`REAL300000042604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042604 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 60, 60, 60, 60, 60, 60, 60, 30, 30, 30, 10, 1, 1, 1, 1, 60, 60, 60, 120] 120
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 230
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042604 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 38, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 38, 60, 60, 60, 60, 1, 1, 1, 2] 120
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 139
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042604 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042604/1 /scratch/stefan/7769623/working/building/REAL300000042604 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/666
`/scratch/stefan/7769623/working/3D/666' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1[O-])

`REAL300000042604.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042604/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042604 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 21, 21, 21] 21
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 40
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042604 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 13, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 21, 21, 21, 21, 1, 1, 1] 21
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 45
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042604 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042604
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042604/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042604/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042604
Building REAL300000042605
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042605'
/scratch/stefan/7769623/working/building/REAL300000042605 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042605

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042605/0 /scratch/stefan/7769623/working/building/REAL300000042605 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/667
`/scratch/stefan/7769623/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Cl)=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042605 none COC1=CC(Cl)=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 144, 144, 144, 144, 144, 144, 144, 144, 3, 3, 3, 1, 1, 1, 13, 13, 13, 66, 144, 144, 144, 144] 144
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 282
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042605 none COC1=CC(Cl)=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 144, 134, 144, 144, 144, 48, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 144, 144, 144, 144, 144, 144, 48, 48, 48, 10, 1, 1, 1, 1] 144
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 255
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042605 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042605
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042605/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042605
Building REAL300000042606
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042606'
/scratch/stefan/7769623/working/building/REAL300000042606 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042606

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042606/0 /scratch/stefan/7769623/working/building/REAL300000042606 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/668
`/scratch/stefan/7769623/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=C(F)C=C1Cl)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042606 none CC(CC1=CC=C(F)C=C1Cl)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 88, 88, 130, 130, 130, 130, 130, 130, 130, 130, 19, 19, 19, 19, 9, 9, 1, 1, 1, 130, 130, 130, 130] 130
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 235
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042606 none CC(CC1=CC=C(F)C=C1Cl)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 16, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [46, 8, 46, 85, 130, 130, 130, 130, 130, 130, 130, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 46, 46, 85, 85, 130, 130, 130, 1, 1, 1, 1] 130
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 429
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042606 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042606
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042606/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042606
Building REAL300000042607
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042607'
/scratch/stefan/7769623/working/building/REAL300000042607 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042607

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042607/0 /scratch/stefan/7769623/working/building/REAL300000042607 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/669
`/scratch/stefan/7769623/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=CC=C3)N(C3CCCC3)N=C2)=C1)

`REAL300000042607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042607 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=CC=C3)N(C3CCCC3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [178, 178, 178, 178, 178, 178, 178, 116, 33, 33, 6, 6, 6, 6, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 178, 178, 178, 178, 116, 33, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 178] 178
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48])
total number of confs: 405
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042607 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=CC=C3)N(C3CCCC3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 127, 127, 160, 160, 127, 160, 160, 127, 127, 178, 178, 178, 178, 127, 127, 1, 1, 1, 1, 13, 67, 160, 160, 127, 160, 160, 178, 178, 178, 178, 178, 178, 178, 178, 178, 127, 1] 178
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 48, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 518
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042607 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=CC=C3)N(C3CCCC3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [160, 160, 160, 160, 160, 160, 160, 91, 22, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 4, 4, 160, 160, 160, 160, 91, 22, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 160] 178
rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 351
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042607 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=CC=C3)N(C3CCCC3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [127, 127, 127, 127, 127, 127, 127, 51, 12, 12, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 6, 6, 6, 6, 1, 1, 127, 127, 127, 127, 51, 12, 4, 4, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 127] 178
rigid atoms, others: [10, 11, 12, 13, 47, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042607 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042607
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042607/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042607
Building REAL300000042608
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042608'
/scratch/stefan/7769623/working/building/REAL300000042608 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042608

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042608/0 /scratch/stefan/7769623/working/building/REAL300000042608 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/670
`/scratch/stefan/7769623/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC=C([N+](=O)[O-])C=C32)=C1)

`REAL300000042608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042608 none O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC=C([N+](=O)[O-])C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 1, 1, 1, 1, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042608 none O=C([O-])C1=CC=CC(NN=C2CCCCC3=CC=C([N+](=O)[O-])C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 24, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 24, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 25
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 40, 24, 25, 26, 27, 28])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042608 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042608
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042608/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042608
Building REAL300000042609
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042609'
/scratch/stefan/7769623/working/building/REAL300000042609 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042609

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042609/0 /scratch/stefan/7769623/working/building/REAL300000042609 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/671
`/scratch/stefan/7769623/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1)

`REAL300000042609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042609 none COC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 140, 140, 140, 140, 140, 140, 140, 140, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 9, 44, 140, 140, 140, 140, 1] 140
rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 242
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042609 none COC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 113, 57, 140, 140, 57, 57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 140, 140, 140, 140, 140, 140, 140, 140, 58, 58, 58, 12, 1, 1, 1, 1, 140] 140
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 544
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042609 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042609
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042609/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042609
Building REAL300000042610
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042610'
/scratch/stefan/7769623/working/building/REAL300000042610 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042610

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042610/0 /scratch/stefan/7769623/working/building/REAL300000042610 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/672
`/scratch/stefan/7769623/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C3OC(F)(F)OC3=C2)=C1)

`REAL300000042610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042610 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3OC(F)(F)OC3=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 1, 1, 13, 43, 43, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 13, 43, 72, 72, 72, 1] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042610 none O=C([O-])C1=CC=CC(NN=CC2=CC=C3OC(F)(F)OC3=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 72, 72, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 47, 8, 1, 1, 1, 72] 72
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042610 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042610
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042610/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042610
Building REAL300000042611
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042611'
/scratch/stefan/7769623/working/building/REAL300000042611 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042611

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042611/0 /scratch/stefan/7769623/working/building/REAL300000042611 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/673
`/scratch/stefan/7769623/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042611 none CN(C)C(=O)C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 8, 10, 1, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 70, 70, 70, 70, 70, 70, 70, 70, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 9, 31, 70, 70, 70, 70] 88
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042611 none CN(C)C(=O)C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 70, 88, 70, 70, 70, 70, 70, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 88, 88, 88, 88, 88, 88, 70, 70, 70, 70, 35, 9, 1, 1, 1, 1] 88
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 179
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042611 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042611
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042611/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042611
Building REAL300000042612
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042612'
/scratch/stefan/7769623/working/building/REAL300000042612 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042612

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042612/0 /scratch/stefan/7769623/working/building/REAL300000042612 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/674
`/scratch/stefan/7769623/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=C(O)C(O)=C1)

`REAL300000042612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042612 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 12, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 67, 67, 67, 67, 67, 67, 67, 67, 28, 28, 28, 8, 1, 1, 1, 1, 67, 67, 67, 67, 134, 134, 67] 268
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 380
number of broken/clashed sets: 203
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042612 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=C(O)C(O)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 12, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
268  conformations in input
total number of sets (complete confs): 268
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 11, 11, 46, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 46, 67, 67, 67, 67, 1, 2, 2, 2, 2, 2, 1] 268
rigid atoms, others: [1, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 163
number of broken/clashed sets: 203
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042612 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042612
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042612/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042612
Building REAL300000042613
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042613'
/scratch/stefan/7769623/working/building/REAL300000042613 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042613

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042613/0 /scratch/stefan/7769623/working/building/REAL300000042613 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/675
`/scratch/stefan/7769623/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=N2)=C1)

`REAL300000042613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042613 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 7, 23, 35, 35, 35, 35, 35, 35, 1] 35
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 56
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042613 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 30, 10, 10, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 30, 10, 4, 4, 1, 1, 1, 1, 35] 35
rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 87
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042613 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 35, 35, 35, 35, 22, 4, 1, 1, 4, 4, 4, 4, 35] 35
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042613 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042613
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042613/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042613
Building REAL300000042614
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042614'
/scratch/stefan/7769623/working/building/REAL300000042614 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042614

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042614/0 /scratch/stefan/7769623/working/building/REAL300000042614 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/676
`/scratch/stefan/7769623/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042614 none CC1=CC=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 22, 22, 48, 52, 52, 52, 52, 52, 52, 52, 52, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 22, 48, 52, 52, 52, 52] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042614 none CC1=CC=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 52, 52, 52, 49, 49, 49, 49, 49, 49, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 52, 52, 52, 52, 52, 49, 49, 49, 49, 32, 7, 1, 1, 1, 1] 52
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 83
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042614 none CC1=CC=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 9, 26, 49, 49, 49, 49] 52
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042614 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042614
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042614/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042614
Building REAL300000042615
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042615'
/scratch/stefan/7769623/working/building/REAL300000042615 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042615

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042615/0 /scratch/stefan/7769623/working/building/REAL300000042615 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/677
`/scratch/stefan/7769623/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OC2(CC1N=NC1=CC=CC(C(=O)[O-])=C1)CC[NH+](C)CC2)

`REAL300000042615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042615 none CC1OC2(CC1N=NC1=CC=CC(C(=O)[O-])=C1)CC[NH+](C)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 5, 5, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 35, 36, 37, 38, 42, 43, 44, 45] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 24, 25, 26, 39, 31])
total number of confs: 33
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042615 none CC1OC2(CC1N=NC1=CC=CC(C(=O)[O-])=C1)CC[NH+](C)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 5, 5, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042615 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042615
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042615/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042615
Building REAL300000042616
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042616'
/scratch/stefan/7769623/working/building/REAL300000042616 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042616

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042616/0 /scratch/stefan/7769623/working/building/REAL300000042616 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/678
`/scratch/stefan/7769623/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCN(C(=O)OCC3=CC=CC=C3)C2)=C1)

`REAL300000042616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042616 none O=C([O-])C1=CC=CC(N=NC2CCN(C(=O)OCC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 52, 52, 72, 201, 201, 201, 201, 201, 201, 35, 1, 1, 1, 1, 35, 35, 35, 35, 35, 201, 201, 201, 201, 201, 201, 201, 35, 35, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 681
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042616 none O=C([O-])C1=CC=CC(N=NC2CCN(C(=O)OCC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 159, 159, 57, 57, 57, 57, 31, 19, 31, 3, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 57, 57, 57, 57, 57, 3, 3, 1, 1, 1, 1, 1, 57, 57, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 350
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042616 none O=C([O-])C1=CC=CC(N=NC2CCN(C(=O)OCC3=CC=CC=C3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 11, 11, 1, 1, 1, 1, 1, 1, 3, 3, 7, 28, 57, 57, 32, 57, 57, 1, 35, 35, 35, 35, 1, 1, 1, 1, 1, 28, 28, 57, 57, 57, 57, 57, 1, 1, 35] 201
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 42, 41, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 43])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042616 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042616
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042616/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042616
Building REAL300000042617
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042617'
/scratch/stefan/7769623/working/building/REAL300000042617 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042617

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042617/0 /scratch/stefan/7769623/working/building/REAL300000042617 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/679
`/scratch/stefan/7769623/working/3D/679' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=N1)

`REAL300000042617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042617 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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: [28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 36, 36, 36, 36, 36, 36, 29, 29, 29, 10, 1, 1, 1, 1, 36, 36, 36] 37
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30])
total number of confs: 72
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042617 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 25, 36, 36, 36, 36, 36, 37, 37, 36, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 36, 36, 36, 36, 1, 1, 1] 37
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 89
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042617 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042617/1 /scratch/stefan/7769623/working/building/REAL300000042617 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/680
`/scratch/stefan/7769623/working/3D/680' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=N1)

`REAL300000042617.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042617/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042617 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 91, 91, 91, 91, 91, 91, 48, 48, 48, 48, 1, 1, 1, 1, 91, 91, 91] 91
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30])
total number of confs: 222
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042617 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 63, 63, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 91, 91, 91, 91, 1, 1, 1] 91
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042617 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042617
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042617/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042617/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042617
Building REAL300000042618
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042618'
/scratch/stefan/7769623/working/building/REAL300000042618 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042618

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042618/0 /scratch/stefan/7769623/working/building/REAL300000042618 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/681
`/scratch/stefan/7769623/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC(OC)=C1O)

`REAL300000042618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042618 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC(OC)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 12, 65, 193, 193, 193, 193, 193, 193, 193, 193, 1, 1, 1, 3, 1, 1, 4, 4, 4, 1, 13, 13, 13, 65, 193, 193, 193, 193, 1, 4, 4, 4, 2] 402
rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 22, 23, 36, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 361
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042618 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC(OC)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 169, 169, 169, 51, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 169, 169, 169, 201, 51, 51, 201, 201, 201, 169, 52, 52, 52, 10, 1, 1, 1, 1, 169, 201, 201, 201, 338] 402
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40])
total number of confs: 905
number of broken/clashed sets: 132
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042618 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042618
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042618/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042618
Building REAL300000042619
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042619'
/scratch/stefan/7769623/working/building/REAL300000042619 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042619

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042619/0 /scratch/stefan/7769623/working/building/REAL300000042619 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/682
`/scratch/stefan/7769623/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(CC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042619 none COC1=CC=C(C(CC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 33, 35, 35, 12, 12, 66, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 2, 2, 2, 1, 1, 33, 33, 35, 35, 35, 35, 35, 35, 35, 66, 108, 108, 108, 108, 1, 1] 116
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 345
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042619 none COC1=CC=C(C(CC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [108, 94, 77, 108, 108, 37, 37, 37, 75, 79, 81, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 108, 108, 108, 108, 108, 108, 108, 75, 75, 81, 81, 81, 81, 81, 81, 81, 8, 1, 1, 1, 1, 108, 108] 116
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 526
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042619 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042619
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042619/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042619
Building REAL300000042620
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042620'
/scratch/stefan/7769623/working/building/REAL300000042620 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042620

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042620/0 /scratch/stefan/7769623/working/building/REAL300000042620 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/683
`/scratch/stefan/7769623/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CN=C2Cl)=C1)

`REAL300000042620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042620 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CN=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 39, 39, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 13, 39, 43, 43, 1] 43
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042620 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CN=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 32, 8, 1, 1, 43] 43
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042620 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042620
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042620/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042620
Building REAL300000042621
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042621'
/scratch/stefan/7769623/working/building/REAL300000042621 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042621

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042621/0 /scratch/stefan/7769623/working/building/REAL300000042621 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/684
`/scratch/stefan/7769623/working/3D/684' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(OC(F)F)=CC=C2Br)=C1)

`REAL300000042621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042621 none O=C([O-])C1=CC=CC(NN=CC2=CC(OC(F)F)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 63, 63, 63, 187, 201, 201, 63, 63, 63, 63, 1, 1, 1, 1, 8, 26, 63, 201, 63, 63, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042621 none O=C([O-])C1=CC=CC(NN=CC2=CC(OC(F)F)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 35, 10, 10, 1, 1, 1, 1, 1, 13, 56, 55, 1, 1, 1, 1, 63, 63, 63, 63, 35, 10, 1, 56, 1, 1, 63] 201
rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20, 21, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 32, 22, 23, 24, 25, 26, 27, 29])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042621 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042621
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042621/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042621
Building REAL300000042622
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042622'
/scratch/stefan/7769623/working/building/REAL300000042622 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042622

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042622/0 /scratch/stefan/7769623/working/building/REAL300000042622 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/685
`/scratch/stefan/7769623/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042622 none COC1=CC=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 37, 37, 38, 38, 37, 3, 3, 3, 1, 1, 1, 1, 7, 37, 37, 37, 37] 38
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 32, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 59
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042622 none COC1=CC=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 38, 37, 37, 37, 37, 12, 1, 1, 1, 1] 38
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042622 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042622
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042622/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042622
Building REAL300000042623
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042623'
/scratch/stefan/7769623/working/building/REAL300000042623 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042623

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042623/0 /scratch/stefan/7769623/working/building/REAL300000042623 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/686
`/scratch/stefan/7769623/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=NNC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042623 none CCOC(=O)C1=NNC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [24, 10, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 35, 87, 87, 87, 87, 87, 87, 87, 87, 1, 24, 24, 24, 24, 24, 1, 7, 35, 87, 87, 87, 87, 1] 152
rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 21, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042623 none CCOC(=O)C1=NNC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [152, 150, 150, 87, 150, 87, 87, 87, 47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 152, 152, 152, 152, 152, 87, 47, 10, 1, 1, 1, 1, 87] 152
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 361
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042623 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042623
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042623/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042623
Building REAL300000042624
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042624'
/scratch/stefan/7769623/working/building/REAL300000042624 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042624

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042624/0 /scratch/stefan/7769623/working/building/REAL300000042624 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/687
`/scratch/stefan/7769623/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1)

`REAL300000042624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042624 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 33, 33, 33, 33, 33, 112, 195, 201, 201, 195, 201, 201, 195, 201, 201, 33, 1, 1, 1, 1, 5, 17, 33, 33, 33, 195, 201, 201, 195, 201, 201, 33, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 44, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 609
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: REAL300000042624 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 160, 99, 99, 43, 43, 43, 43, 43, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 43, 201, 201, 201, 201, 160, 99, 43, 43, 43, 3, 1, 1, 1, 1, 1, 43, 201] 201
rigid atoms, others: [38, 39, 40, 41, 42, 17, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44])
total number of confs: 493
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042624 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 32, 33, 33, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 11, 31, 45, 45, 31, 43, 43, 31, 43, 43, 1, 33, 32, 33, 33, 18, 6, 1, 1, 1, 31, 43, 43, 31, 43, 43, 1, 33] 201
rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44])
total number of confs: 282
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042624 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042624
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042624/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042624
Building REAL300000042625
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042625'
/scratch/stefan/7769623/working/building/REAL300000042625 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042625

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042625/0 /scratch/stefan/7769623/working/building/REAL300000042625 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/688
`/scratch/stefan/7769623/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=C2C=CC=C3[N+](=O)[O-])=C1)

`REAL300000042625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042625 none O=C([O-])C1=CC=CC(NN=C2CCC3=C2C=CC=C3[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 1] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042625 none O=C([O-])C1=CC=CC(NN=C2CCC3=C2C=CC=C3[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 24, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 25, 24, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25] 25
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 47
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042625 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042625
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042625/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042625
Building REAL300000042626
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042626'
/scratch/stefan/7769623/working/building/REAL300000042626 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042626

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042626/0 /scratch/stefan/7769623/working/building/REAL300000042626 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/689
`/scratch/stefan/7769623/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=CN1)

`REAL300000042626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042626 none COC(=O)C1=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 8, 8, 30, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 8, 8, 8, 2, 2, 2, 8, 30, 45, 45, 45, 45, 1, 1] 67
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 34, 20, 21] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042626 none COC(=O)C1=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=CN1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 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, 45, 67, 45, 45, 45, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 67, 67, 67, 45, 45, 45, 26, 8, 1, 1, 1, 1, 45, 45] 67
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 156
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042626 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042626
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042626/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042626
Building REAL300000042627
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042627'
/scratch/stefan/7769623/working/building/REAL300000042627 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042627

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042627/0 /scratch/stefan/7769623/working/building/REAL300000042627 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/690
`/scratch/stefan/7769623/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1C)

`REAL300000042627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042627 none CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 25, 25, 118, 160, 160, 160, 160, 160, 160, 160, 160, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 24, 118, 160, 160, 160, 160, 1, 2, 2, 2] 160
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 368
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042627 none CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [159, 159, 160, 160, 131, 131, 131, 131, 65, 65, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 131, 160, 160, 160, 160, 160, 160, 160, 160, 131, 65, 12, 1, 1, 1, 1, 160, 160, 160, 160] 160
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 268
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042627 none CC1=CC=C(C2=NC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)S2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 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, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 53, 131, 131, 131, 131, 131, 132, 132, 131, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 53, 131, 131, 131, 131, 5, 5, 5, 5] 160
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 249
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042627 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042627
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042627/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042627
Building REAL300000042628
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042628'
/scratch/stefan/7769623/working/building/REAL300000042628 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042628

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042628/0 /scratch/stefan/7769623/working/building/REAL300000042628 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/691
`/scratch/stefan/7769623/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042628 none CC1=NN(C2=CC=CC=C2F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 8, 1, 1, 1, 8, 8, 44, 79, 79, 79, 79, 79, 80, 80, 79, 2, 2, 2, 8, 8, 7, 7, 1, 8, 44, 79, 79, 79, 79] 110
rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 185
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042628 none CC1=NN(C2=CC=CC=C2F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [79, 79, 79, 79, 79, 109, 109, 109, 109, 109, 110, 79, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 80, 80, 109, 109, 109, 110, 79, 32, 8, 1, 1, 1, 1] 110
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 180
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042628 none CC1=NN(C2=CC=CC=C2F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 37, 93, 109, 109, 109, 109, 110, 110, 110, 110, 8, 8, 8, 1, 1, 1, 1, 8, 38, 94, 109, 109, 109, 110] 110
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 279
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042628 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042628
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042628/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042628
Building REAL300000042629
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042629'
/scratch/stefan/7769623/working/building/REAL300000042629 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042629

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042629/0 /scratch/stefan/7769623/working/building/REAL300000042629 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/692
`/scratch/stefan/7769623/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042629 none CC1=NN(C2=CC=CC=C2Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 10, 1, 1, 1, 10, 10, 58, 97, 97, 97, 97, 97, 98, 98, 97, 2, 2, 2, 10, 9, 9, 9, 1, 10, 58, 97, 97, 97, 97] 177
rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042629 none CC1=NN(C2=CC=CC=C2Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [97, 97, 97, 97, 97, 177, 177, 177, 177, 177, 177, 97, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 98, 98, 98, 177, 177, 177, 177, 97, 36, 8, 1, 1, 1, 1] 177
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 273
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042629 none CC1=NN(C2=CC=CC=C2Br)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 48, 148, 177, 177, 177, 177, 177, 177, 177, 177, 10, 10, 10, 1, 1, 1, 1, 9, 48, 148, 177, 177, 177, 177] 177
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042629 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042629
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042629/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042629
Building REAL300000042630
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042630'
/scratch/stefan/7769623/working/building/REAL300000042630 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042630

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042630/0 /scratch/stefan/7769623/working/building/REAL300000042630 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/693
`/scratch/stefan/7769623/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042630 none CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 10, 10, 10, 10, 10, 11, 1, 1, 1, 7, 7, 47, 67, 67, 67, 67, 67, 68, 68, 67, 2, 2, 2, 11, 11, 10, 11, 1, 7, 47, 67, 67, 67, 67] 139
rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042630 none CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [67, 67, 67, 67, 67, 139, 139, 139, 139, 139, 139, 67, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 68, 68, 139, 139, 139, 139, 67, 28, 8, 1, 1, 1, 1] 139
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 228
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042630 none CC1=NN(C2=CC=CC=C2Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 43, 43, 118, 139, 139, 139, 139, 139, 139, 139, 139, 11, 11, 11, 1, 1, 1, 1, 10, 43, 118, 139, 139, 139, 139] 139
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 349
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042630 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042630
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042630/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042630
Building REAL300000042631
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042631'
/scratch/stefan/7769623/working/building/REAL300000042631 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042631

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042631/0 /scratch/stefan/7769623/working/building/REAL300000042631 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/694
`/scratch/stefan/7769623/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042631 none CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 1, 7, 7, 58, 98, 98, 98, 98, 98, 98, 98, 98, 2, 2, 2, 3, 3, 4, 4, 4, 3, 3, 1, 7, 58, 98, 98, 98, 98] 98
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 35] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042631 none CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 51, 12, 1, 1, 1, 1] 98
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 153
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042631 none CC1=NN(C2=CC=C(C)C=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 17, 17, 73, 98, 98, 98, 98, 98, 98, 98, 98, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 3, 17, 72, 98, 98, 98, 98] 98
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042631 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042631
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042631/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042631
Building REAL300000042632
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042632'
/scratch/stefan/7769623/working/building/REAL300000042632 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042632

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042632/0 /scratch/stefan/7769623/working/building/REAL300000042632 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/695
`/scratch/stefan/7769623/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC(Br)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042632 none CC1=NN(C2=CC=CC(Br)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 8, 8, 42, 63, 63, 63, 63, 63, 63, 63, 62, 2, 2, 2, 7, 7, 6, 7, 1, 8, 42, 63, 63, 63, 62] 115
rigid atoms, others: [0, 1, 2, 3, 4, 32, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 149
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042632 none CC1=NN(C2=CC=CC(Br)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [62, 62, 62, 62, 62, 115, 115, 115, 115, 115, 115, 62, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 63, 63, 115, 115, 115, 115, 62, 28, 8, 1, 1, 1, 1] 115
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 210
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042632 none CC1=NN(C2=CC=CC(Br)=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 37, 97, 115, 115, 115, 115, 115, 115, 115, 115, 7, 7, 7, 1, 1, 1, 1, 7, 37, 97, 115, 115, 115, 115] 115
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 274
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042632 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042632
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042632/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042632
Building REAL300000042633
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042633'
/scratch/stefan/7769623/working/building/REAL300000042633 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042633

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042633/0 /scratch/stefan/7769623/working/building/REAL300000042633 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/696
`/scratch/stefan/7769623/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)C=C2)=C1)

`REAL300000042633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042633 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 60, 60, 115, 115, 115, 117, 117, 117, 117, 117, 115, 115, 1, 1, 1, 1, 13, 60, 115, 117, 117, 117, 117, 117, 115, 115, 1] 117
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042633 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [117, 117, 117, 117, 117, 117, 117, 94, 31, 31, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 117, 117, 117, 117, 94, 31, 6, 1, 1, 1, 1, 1, 6, 6, 117] 117
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 269
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042633 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 115, 115, 115, 115, 53, 10, 10, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 115, 115, 115, 115, 52, 10, 1, 6, 6, 2, 6, 6, 1, 1, 115] 117
rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36])
total number of confs: 230
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042633 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042633
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042633/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042633
Building REAL300000042634
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042634'
/scratch/stefan/7769623/working/building/REAL300000042634 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042634

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042634/0 /scratch/stefan/7769623/working/building/REAL300000042634 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/697
`/scratch/stefan/7769623/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1)

`REAL300000042634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 45, 23, 23, 5, 5, 5, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 54, 54, 54, 54, 45, 23, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 54] 54
rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 128
number of broken/clashed sets: 0
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 47, 47, 54, 54, 47, 47, 54, 54, 47, 54, 54, 47, 47, 1, 1, 1, 1, 8, 23, 54, 54, 54, 54, 54, 54, 54, 47, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 45, 19, 19, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 4, 4, 54, 54, 54, 54, 45, 19, 1, 1, 1, 1, 1, 6, 6, 4, 6, 6, 54] 54
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 133
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 47, 47, 47, 47, 47, 37, 13, 13, 1, 1, 1, 1, 4, 4, 1, 1, 5, 5, 1, 5, 5, 1, 1, 47, 47, 47, 47, 37, 13, 4, 4, 4, 4, 4, 5, 5, 1, 5, 5, 47] 54
rigid atoms, others: [10, 11, 12, 13, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 124
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042634 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042634/1 /scratch/stefan/7769623/working/building/REAL300000042634 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/698
`/scratch/stefan/7769623/working/3D/698' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1)

`REAL300000042634.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042634/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(N=NCC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 112, 112, 21, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 167, 167, 167, 167, 21, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 167] 167
rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 278
number of broken/clashed sets: 1
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(N=NCC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 52, 128, 128, 167, 167, 128, 128, 167, 167, 128, 167, 167, 128, 128, 1, 1, 1, 1, 52, 51, 167, 167, 167, 167, 167, 167, 167, 128, 167, 167, 1] 167
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 616
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: REAL300000042634 none O=C([O-])C1=CC=CC(N=NCC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 86, 86, 13, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 3, 3, 167, 167, 167, 167, 13, 13, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 167] 167
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 267
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042634 none O=C([O-])C1=CC=CC(N=NCC2=C(C3CC3)N(C3=CC=CC=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 128, 128, 128, 128, 55, 55, 8, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 1, 5, 5, 1, 1, 128, 128, 128, 128, 8, 8, 3, 3, 3, 3, 3, 5, 5, 1, 5, 5, 128] 167
rigid atoms, others: [10, 11, 12, 13, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 207
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042634 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042634
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042634/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042634/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042634
Building REAL300000042635
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042635'
/scratch/stefan/7769623/working/building/REAL300000042635 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042635

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042635/0 /scratch/stefan/7769623/working/building/REAL300000042635 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/699
`/scratch/stefan/7769623/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(Cl)=C(Br)C=C32)=CC=C1)

`REAL300000042635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042635 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(Cl)=C(Br)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 16, 1, 17, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 13, 19, 19, 19, 1, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042635 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(Cl)=C(Br)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 16, 1, 17, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 8, 1, 1, 1, 19, 19, 19] 19
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 33
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042635 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042635
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042635/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042635
Building REAL300000042636
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042636'
/scratch/stefan/7769623/working/building/REAL300000042636 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042636

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042636/0 /scratch/stefan/7769623/working/building/REAL300000042636 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/700
`/scratch/stefan/7769623/working/3D/700' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)C=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042636 none CC1=C(Br)C=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 19, 19, 18, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 18] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042636 none CC1=C(Br)C=CC2=C1NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 19, 18, 18, 18, 10, 1, 1, 1, 1] 19
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042636 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042636
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042636/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042636
Building REAL300000042637
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042637'
/scratch/stefan/7769623/working/building/REAL300000042637 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042637

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042637/0 /scratch/stefan/7769623/working/building/REAL300000042637 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/701
`/scratch/stefan/7769623/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C#N)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042637 none CC(C)(C#N)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 40, 85, 85, 85, 85, 85, 86, 86, 85, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 7, 40, 85, 85, 85, 85, 1, 1] 167
rigid atoms, others: [1, 5, 6, 7, 8, 9, 21, 22, 38, 29, 30, 37] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042637 none CC(C)(C#N)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 86, 167, 167, 167, 79, 86, 85, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 86, 167, 167, 167, 167, 167, 167, 86, 85, 44, 10, 1, 1, 1, 1, 86, 86] 167
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 575
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042637 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042637
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042637/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042637
Building REAL300000042638
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042638'
/scratch/stefan/7769623/working/building/REAL300000042638 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042638

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042638/0 /scratch/stefan/7769623/working/building/REAL300000042638 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/702
`/scratch/stefan/7769623/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)O1)

`REAL300000042638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042638 none COC(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [13, 13, 1, 13, 1, 1, 1, 1, 8, 8, 40, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 13, 13, 13, 1, 8, 39, 63, 63, 63, 62, 2, 2, 2] 98
rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 21, 25] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042638 none COC(=O)C1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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, 62, 98, 62, 62, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 62, 63, 62, 98, 98, 98, 62, 32, 8, 1, 1, 1, 1, 63, 63, 63] 98
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042638 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042638
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042638/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042638
Building REAL300000042639
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042639'
/scratch/stefan/7769623/working/building/REAL300000042639 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042639

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042639/0 /scratch/stefan/7769623/working/building/REAL300000042639 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/703
`/scratch/stefan/7769623/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Br)=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1O)

`REAL300000042639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042639 none COC1=CC(Br)=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 69, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 1, 1, 13, 13, 13, 69, 201, 201, 201, 201, 2] 402
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 350
number of broken/clashed sets: 221
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042639 none COC1=CC(Br)=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 201, 201, 201, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 200, 201, 51, 51, 51, 11, 1, 1, 1, 1, 402] 402
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 678
number of broken/clashed sets: 221
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042639 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042639
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042639/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042639
Building REAL300000042640
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042640'
/scratch/stefan/7769623/working/building/REAL300000042640 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042640

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042640/0 /scratch/stefan/7769623/working/building/REAL300000042640 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/704
`/scratch/stefan/7769623/working/3D/704' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042640 none N#CC1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 19, 19, 18, 1, 1, 1, 1, 7, 18, 18, 18, 18] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 35
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042640 none N#CC1=CC=C2C(=C1)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 18, 18, 18, 10, 1, 1, 1, 1] 19
rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042640 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042640
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042640/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042640
Building REAL300000042641
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042641'
/scratch/stefan/7769623/working/building/REAL300000042641 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042641

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042641/0 /scratch/stefan/7769623/working/building/REAL300000042641 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/705
`/scratch/stefan/7769623/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=CNC1=O)

`REAL300000042641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042641 none N#CC1=C2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=CNC1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 1, 1] 26
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31])
total number of confs: 43
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042641 none N#CC1=C2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=CNC1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 1, 1, 1, 1, 26, 26] 26
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 48
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042641 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042641/1 /scratch/stefan/7769623/working/building/REAL300000042641 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/706
`/scratch/stefan/7769623/working/3D/706' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C[N-]C1=O)

`REAL300000042641.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042641/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042641 none N#CC1=C2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C[N-]C1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31])
total number of confs: 30
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042641 none N#CC1=C2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C[N-]C1=O NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 15] 15
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 29
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042641 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042641
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042641/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042641/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042641
Building REAL300000042642
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042642'
/scratch/stefan/7769623/working/building/REAL300000042642 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042642

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042642/0 /scratch/stefan/7769623/working/building/REAL300000042642 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/707
`/scratch/stefan/7769623/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2C(=C1)C(=NNC1=CC=CC(C(=O)[O-])=C1)C(=O)N2C)

`REAL300000042642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042642 none COC1=CC=C2C(=C1)C(=NNC1=CC=CC(C(=O)[O-])=C1)C(=O)N2C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 30, 30, 31, 31, 30, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 30, 30, 30, 30, 1, 1, 1] 31
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 20, 21, 22, 23, 36, 27, 28, 29, 37] set([0, 32, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31])
total number of confs: 51
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042642 none COC1=CC=C2C(=C1)C(=NNC1=CC=CC(C(=O)[O-])=C1)C(=O)N2C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 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, 30, 30, 30, 30, 30, 30, 30, 30, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 30, 30, 31, 31, 31, 30, 30, 30, 12, 1, 1, 1, 1, 31, 30, 30] 31
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042642 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042642
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042642/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042642
Building REAL300000042643
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042643'
/scratch/stefan/7769623/working/building/REAL300000042643 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042643

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042643/0 /scratch/stefan/7769623/working/building/REAL300000042643 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/708
`/scratch/stefan/7769623/working/3D/708' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C=C1)

`REAL300000042643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042643 none CC(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [63, 59, 63, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 61, 61, 54, 61, 61, 61, 63, 63, 63, 63, 63, 63, 63, 59, 59, 8, 1, 1, 1, 1, 61, 61, 61, 61] 66
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 284
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042643 none CC(C)CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [19, 18, 19, 7, 1, 7, 7, 31, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 18, 18, 31, 61, 61, 61, 61, 1, 1, 1, 1] 66
rigid atoms, others: [4, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 177
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042643 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042643
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042643/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042643
Building REAL300000042644
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042644'
/scratch/stefan/7769623/working/building/REAL300000042644 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042644

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042644/0 /scratch/stefan/7769623/working/building/REAL300000042644 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/709
`/scratch/stefan/7769623/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1)

`REAL300000042644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042644 none CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 3, 5, 5, 3, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 32, 32, 32, 32, 1, 1, 3, 3, 5, 5, 5, 5, 5] 40
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 40, 39, 34, 16, 17, 18, 19, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 78
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: REAL300000042644 none CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 28, 28, 40, 40, 40, 40, 40, 40, 40, 40, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 5, 5, 2, 2, 1, 1, 1, 1, 1] 40
rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 67
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042644 none CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 32, 32, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 32, 32, 32, 40, 40, 40, 40, 40, 40, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 32, 32, 40, 40, 40, 40, 40, 40, 40] 40
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 15, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 122
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042644 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042644/1 /scratch/stefan/7769623/working/building/REAL300000042644 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/710
`/scratch/stefan/7769623/working/3D/710' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1)

`REAL300000042644.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042644/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042644 none CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 12, 12, 30, 30, 30, 31, 31, 31, 31, 31, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 30, 30, 30, 31, 1, 1, 3, 3, 5, 5, 5, 5, 5] 37
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 40, 39, 34, 16, 17, 18, 19, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 68
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: REAL300000042644 none CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 25, 25, 37, 37, 37, 37, 37, 37, 37, 37, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 5, 5, 2, 2, 1, 1, 1, 1, 1] 37
rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 61
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042644 none CC1(C)CC(N=NC2=CC=CC(C(=O)[O-])=C2)C[N@H+]1CC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 31, 31, 31, 31, 31, 31, 31, 31, 30, 1, 1, 1, 1, 31, 31, 37, 37, 37, 37, 37, 37, 37] 37
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 15, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 108
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042644 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042644
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042644/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042644/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042644
Building REAL300000042645
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042645'
/scratch/stefan/7769623/working/building/REAL300000042645 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042645

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042645/0 /scratch/stefan/7769623/working/building/REAL300000042645 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/711
`/scratch/stefan/7769623/working/3D/711' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CS1)

`REAL300000042645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042645 none CN(C)CC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 20, 1, 1, 1, 1, 1, 8, 8, 32, 68, 68, 68, 68, 68, 69, 69, 68, 1, 1, 20, 20, 20, 20, 20, 20, 8, 8, 8, 32, 68, 68, 68, 68, 1] 138
rigid atoms, others: [35, 3, 4, 5, 6, 7, 19, 20] set([0, 1, 2, 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: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042645 none CN(C)CC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 126, 138, 68, 68, 68, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 68, 138, 138, 138, 138, 138, 138, 126, 126, 38, 8, 1, 1, 1, 1, 68] 138
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042645 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042645
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042645/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042645
Building REAL300000042646
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042646'
/scratch/stefan/7769623/working/building/REAL300000042646 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042646

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042646/0 /scratch/stefan/7769623/working/building/REAL300000042646 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/712
`/scratch/stefan/7769623/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1OC(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042646 none COC1=CC=CC2=C1OC(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 54, 54, 54, 54, 54, 54, 54, 54, 3, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 54, 54, 54, 54] 54
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 38, 28, 29, 30, 37] set([0, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 87
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042646 none COC1=CC=CC2=C1OC(C)(C)CC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 10, 1, 1, 1, 1] 54
rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 78
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042646 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042646
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042646/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042646
Building REAL300000042647
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042647'
/scratch/stefan/7769623/working/building/REAL300000042647 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042647

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042647/0 /scratch/stefan/7769623/working/building/REAL300000042647 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/713
`/scratch/stefan/7769623/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042647 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 48, 80, 80, 80, 80, 80, 81, 81, 80, 1, 5, 5, 1, 1, 8, 48, 80, 80, 80, 80] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 23, 24] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 180
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042647 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 80, 201, 201, 80, 80, 80, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 201, 201, 80, 80, 48, 12, 1, 1, 1, 1] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 659
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042647 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042647
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042647/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042647
Building REAL300000042648
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042648'
/scratch/stefan/7769623/working/building/REAL300000042648 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042648

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042648/0 /scratch/stefan/7769623/working/building/REAL300000042648 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/714
`/scratch/stefan/7769623/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC12CC2)

`REAL300000042648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042648 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC12CC2 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 13, 13, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1] 92
rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 44, 45, 46, 47, 48, 49, 25, 22, 23, 24, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 90
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042648 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC12CC2 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 92, 70, 38, 70, 38, 38, 38, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 38, 38, 92, 92, 92, 92, 92, 92, 92, 92, 92, 38, 38, 38, 38, 38, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38] 92
rigid atoms, others: [40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49])
total number of confs: 237
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042648 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042648
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042648/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042648
Building REAL300000042649
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042649'
/scratch/stefan/7769623/working/building/REAL300000042649 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042649

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042649/0 /scratch/stefan/7769623/working/building/REAL300000042649 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/715
`/scratch/stefan/7769623/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1)

`REAL300000042649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042649 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 59, 59, 58, 58, 59, 59, 58, 59, 59, 59, 59, 40, 40, 40, 10, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59] 59
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 113
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042649 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [13, 3, 13, 13, 34, 59, 59, 59, 59, 59, 59, 59, 59, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 34, 59, 59, 59, 59, 3, 3, 1, 1, 1, 1, 1, 3] 59
rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40])
total number of confs: 124
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042649 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 1, 10, 10, 29, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 29, 59, 59, 59, 59, 1, 1, 3, 3, 2, 3, 3, 1] 59
rigid atoms, others: [1, 34, 33, 40, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 122
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042649 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042649/1 /scratch/stefan/7769623/working/building/REAL300000042649 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/716
`/scratch/stefan/7769623/working/3D/716' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1)

`REAL300000042649.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042649/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042649 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 66, 66, 66, 66, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155] 155
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042649 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [22, 3, 22, 106, 106, 155, 155, 155, 155, 155, 155, 155, 155, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 22, 22, 22, 22, 155, 155, 155, 155, 3, 3, 1, 1, 1, 1, 1, 3] 155
rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40])
total number of confs: 257
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042649 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 12, 78, 78, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 12, 12, 12, 12, 155, 155, 155, 155, 1, 1, 3, 3, 3, 3, 3, 1] 155
rigid atoms, others: [1, 34, 33, 40, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042649 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042649
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042649/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042649/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042649
Building REAL300000042650
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042650'
/scratch/stefan/7769623/working/building/REAL300000042650 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042650

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042650/0 /scratch/stefan/7769623/working/building/REAL300000042650 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/717
`/scratch/stefan/7769623/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=NN2C2=CC=CC=C2)=C1)

`REAL300000042650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042650 none O=C([O-])C1=CC=CC(NN=CC2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 163, 163, 163, 163, 163, 168, 168, 163, 168, 168, 1, 1, 1, 1, 13, 72, 163, 168, 168, 163, 168, 168, 1] 168
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 253
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042650 none O=C([O-])C1=CC=CC(NN=CC2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 168, 168, 168, 168, 102, 25, 25, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 102, 25, 5, 1, 1, 1, 1, 1, 168] 168
rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 350
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042650 none O=C([O-])C1=CC=CC(NN=CC2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [163, 163, 163, 163, 162, 163, 163, 74, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 163, 162, 163, 163, 74, 12, 1, 5, 5, 1, 5, 5, 163] 168
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 323
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042650 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042650
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042650/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042650
Building REAL300000042651
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042651'
/scratch/stefan/7769623/working/building/REAL300000042651 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042651

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042651/0 /scratch/stefan/7769623/working/building/REAL300000042651 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/718
`/scratch/stefan/7769623/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(OC)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F)

`REAL300000042651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042651 none COC1=CC(OC)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 1, 1, 12, 12, 59, 165, 165, 165, 165, 165, 165, 165, 165, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 12, 59, 165, 165, 165, 165, 1] 196
rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 20, 21, 22, 36, 26] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042651 none COC1=CC(OC)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 100, 99, 165, 165, 165, 196, 80, 80, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 165, 165, 165, 196, 196, 196, 165, 196, 196, 196, 80, 12, 1, 1, 1, 1, 165] 196
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 601
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042651 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042651
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042651/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042651
Building REAL300000042652
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042652'
/scratch/stefan/7769623/working/building/REAL300000042652 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042652

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042652/0 /scratch/stefan/7769623/working/building/REAL300000042652 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/719
`/scratch/stefan/7769623/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(F)C(Cl)=C32)=C1)

`REAL300000042652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042652 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(F)C(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042652 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(F)C(Cl)=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 10, 1, 1, 1, 1, 1, 1, 17] 17
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 32
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042652 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042652
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042652/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042652
Building REAL300000042653
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042653'
/scratch/stefan/7769623/working/building/REAL300000042653 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042653

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042653/0 /scratch/stefan/7769623/working/building/REAL300000042653 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/720
`/scratch/stefan/7769623/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC)

`REAL300000042653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042653 none COC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 45, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 3, 4, 4, 4, 1, 11, 45, 111, 111, 111, 111, 1, 4, 4, 4] 143
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 19, 20, 21, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042653 none COC1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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, 111, 111, 111, 111, 111, 66, 66, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 111, 111, 111, 143, 143, 143, 143, 111, 66, 12, 1, 1, 1, 1, 111, 143, 143, 143] 143
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042653 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042653
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042653/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042653
Building REAL300000042654
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042654'
/scratch/stefan/7769623/working/building/REAL300000042654 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042654

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042654/0 /scratch/stefan/7769623/working/building/REAL300000042654 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/721
`/scratch/stefan/7769623/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1)

`REAL300000042654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042654 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 9, 9, 38, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 5, 5, 1, 1, 9, 38, 67, 67, 67, 67, 1] 147
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 20, 21, 22, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31, 32])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042654 none NS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 66, 147, 147, 55, 67, 67, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 67, 147, 147, 67, 67, 46, 11, 1, 1, 1, 1, 67] 147
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 530
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042654 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042654
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042654/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042654
Building REAL300000042655
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042655'
/scratch/stefan/7769623/working/building/REAL300000042655 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042655

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042655/0 /scratch/stefan/7769623/working/building/REAL300000042655 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/722
`/scratch/stefan/7769623/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C(Br)=C1)

`REAL300000042655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042655 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 91, 91, 89, 91, 91, 91, 91, 50, 50, 50, 10, 1, 1, 1, 1, 91, 91, 182, 91] 182
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 336
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042655 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 55, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 91, 91, 91, 91, 1, 1, 2, 1] 182
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 193
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042655 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042655/1 /scratch/stefan/7769623/working/building/REAL300000042655 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/723
`/scratch/stefan/7769623/working/3D/723' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C(Br)=C1)

`REAL300000042655.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042655/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042655 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 47, 47, 45, 46, 47, 47, 47, 24, 24, 24, 5, 1, 1, 1, 1, 47, 47, 47] 47
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042655 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([O-])C(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 41, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 47, 47, 47, 47, 1, 1, 1] 47
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 109
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042655 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042655
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042655/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042655/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042655
Building REAL300000042656
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042656'
/scratch/stefan/7769623/working/building/REAL300000042656 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042656

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042656/0 /scratch/stefan/7769623/working/building/REAL300000042656 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/724
`/scratch/stefan/7769623/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3F)=C2)=C1)

`REAL300000042656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042656 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 60, 60, 60, 60, 60, 95, 95, 201, 201, 95, 201, 201, 201, 201, 60, 1, 1, 1, 1, 7, 26, 60, 60, 60, 95, 95, 201, 201, 201, 60, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 709
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042656 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 168, 78, 77, 16, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 168, 78, 15, 15, 15, 8, 8, 1, 1, 1, 15, 201] 201
rigid atoms, others: [38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42])
total number of confs: 518
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042656 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OCC3=CC=C(F)C=C3F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 59, 60, 60, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 2, 15, 15, 15, 16, 1, 60, 59, 60, 60, 28, 6, 1, 1, 1, 2, 2, 15, 15, 16, 1, 60] 201
rigid atoms, others: [33, 34, 35, 41, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 42])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042656 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042656
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042656/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042656
Building REAL300000042657
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042657'
/scratch/stefan/7769623/working/building/REAL300000042657 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042657

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042657/0 /scratch/stefan/7769623/working/building/REAL300000042657 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/725
`/scratch/stefan/7769623/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042657 none CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 2, 7, 7, 1, 1, 1, 9, 9, 45, 63, 63, 63, 63, 63, 63, 63, 63, 2, 2, 2, 7, 7, 7, 7, 6, 7, 7, 1, 9, 45, 63, 63, 63, 63] 113
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 35] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042657 none CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 113, 113, 113, 113, 113, 113, 63, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 63, 63, 113, 113, 113, 113, 113, 113, 113, 63, 28, 8, 1, 1, 1, 1] 113
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 200
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042657 none CC1=NN(C2=CC(C)=CC=C2)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 37, 97, 112, 113, 113, 113, 113, 113, 113, 113, 7, 7, 7, 1, 2, 2, 2, 1, 1, 1, 7, 37, 97, 113, 113, 113, 113] 113
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 279
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042657 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042657
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042657/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042657
Building REAL300000042658
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042658'
/scratch/stefan/7769623/working/building/REAL300000042658 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042658

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042658/0 /scratch/stefan/7769623/working/building/REAL300000042658 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/726
`/scratch/stefan/7769623/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC([N+](=O)[O-])=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042658 none COC1=CC([N+](=O)[O-])=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 147, 147, 147, 147, 147, 148, 148, 147, 4, 4, 4, 1, 1, 1, 13, 13, 13, 67, 147, 147, 147, 147] 148
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 300
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042658 none COC1=CC([N+](=O)[O-])=CC=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 147, 147, 147, 141, 147, 147, 147, 147, 147, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 148, 148, 148, 147, 147, 147, 54, 54, 54, 10, 1, 1, 1, 1] 148
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 254
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042658 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042658
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042658/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042658
Building REAL300000042659
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042659'
/scratch/stefan/7769623/working/building/REAL300000042659 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042659

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042659/0 /scratch/stefan/7769623/working/building/REAL300000042659 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/727
`/scratch/stefan/7769623/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C2=CC=CC=C2C(Br)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042659 none CN1C2=CC=CC=C2C(Br)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 1, 10, 36, 49, 49, 49, 49] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 117
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042659 none CN1C2=CC=CC=C2C(Br)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 49, 49, 49, 38, 12, 1, 1, 1, 1] 49
rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042659 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042659
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042659/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042659
Building REAL300000042660
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042660'
/scratch/stefan/7769623/working/building/REAL300000042660 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042660

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042660/0 /scratch/stefan/7769623/working/building/REAL300000042660 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/728
`/scratch/stefan/7769623/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)CCO1)

`REAL300000042660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042660 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 97, 97, 97, 151, 151, 201, 201, 201, 201, 97, 97, 97, 43, 43, 43, 43, 1, 1, 1, 1, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 97] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 584
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042660 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 48, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 1, 1, 5, 5, 12, 14, 14, 14, 1, 1, 1, 8, 8, 8, 7, 97, 97, 97, 97, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 48, 13, 14, 15, 16, 49, 46, 23, 24, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 204
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042660 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042660
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042660/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042660
Building REAL300000042661
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042661'
/scratch/stefan/7769623/working/building/REAL300000042661 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042661

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042661/0 /scratch/stefan/7769623/working/building/REAL300000042661 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/729
`/scratch/stefan/7769623/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)NS(=O)(=O)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC1)

`REAL300000042661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042661 none CC(C)(C)NS(=O)(=O)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [8, 5, 8, 8, 5, 1, 5, 5, 1, 1, 7, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 7, 7, 38, 38, 38, 38, 1, 1, 1, 1] 54
rigid atoms, others: [5, 39, 8, 9, 42, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 101
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042661 none CC(C)(C)NS(=O)(=O)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 38, 54, 54, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 17, 17, 1, 1, 1, 1, 38, 38, 38, 38] 54
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 207
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042661 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042661
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042661/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042661
Building REAL300000042662
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042662'
/scratch/stefan/7769623/working/building/REAL300000042662 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042662

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042662/0 /scratch/stefan/7769623/working/building/REAL300000042662 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/730
`/scratch/stefan/7769623/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NNC2=CS(=O)(=O)CC3=CC=CC=C32)=C1)

`REAL300000042662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042662 none O=C([O-])C1=CC=CC(NNC2=CS(=O)(=O)CC3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 13, 41, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 13, 41, 70, 70, 70, 70, 70, 70, 70, 1] 70
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042662 none O=C([O-])C1=CC=CC(NNC2=CS(=O)(=O)CC3=CC=CC=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 70, 70, 70, 70, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 29, 9, 1, 1, 1, 1, 1, 1, 1, 70] 70
rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27])
total number of confs: 137
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042662 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042662
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042662/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042662
Building REAL300000042663
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042663'
/scratch/stefan/7769623/working/building/REAL300000042663 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042663

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042663/0 /scratch/stefan/7769623/working/building/REAL300000042663 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/731
`/scratch/stefan/7769623/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1)

`REAL300000042663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042663 none CCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 6, 1, 1, 1, 1, 1, 1, 12, 12, 42, 82, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 28, 29, 29, 28, 28, 14, 14, 1, 1, 12, 42, 82, 82, 82, 82, 2, 2, 2, 1] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 20, 21, 22, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 280
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042663 none CCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 188, 43, 34, 82, 82, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 82, 82, 201, 201, 201, 201, 201, 201, 201, 82, 82, 34, 8, 1, 1, 1, 1, 82, 82, 82, 82] 201
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 481
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042663 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042663
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042663/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042663
Building REAL300000042664
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042664'
/scratch/stefan/7769623/working/building/REAL300000042664 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042664

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042664/0 /scratch/stefan/7769623/working/building/REAL300000042664 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/732
`/scratch/stefan/7769623/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C2N1C)

`REAL300000042664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042664 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C2N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 12, 12, 61, 85, 85, 85, 85, 85, 86, 86, 85, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 61, 85, 85, 85, 85, 1, 1, 1, 1, 2, 2, 2] 86
rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042664 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=CC=C2N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [85, 85, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 85, 85, 85, 85, 85, 85, 85, 86, 86, 86, 38, 12, 1, 1, 1, 1, 85, 85, 85, 85, 86, 86, 86] 86
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 144
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042664 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042664
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042664/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042664
Building REAL300000042665
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042665'
/scratch/stefan/7769623/working/building/REAL300000042665 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042665

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042665/0 /scratch/stefan/7769623/working/building/REAL300000042665 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/733
`/scratch/stefan/7769623/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC1=CC=C(Br)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042665 none CCC(CC1=CC=C(Br)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [18, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 53, 53, 124, 124, 124, 124, 124, 124, 124, 124, 18, 19, 19, 18, 19, 10, 3, 3, 1, 1, 1, 1, 124, 124, 124, 124] 126
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 239
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042665 none CCC(CC1=CC=C(Br)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [69, 55, 8, 55, 110, 124, 124, 110, 115, 124, 124, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 85, 85, 85, 85, 55, 110, 110, 124, 124, 124, 124, 1, 1, 1, 1] 126
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 773
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042665 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042665
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042665/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042665
Building REAL300000042666
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042666'
/scratch/stefan/7769623/working/building/REAL300000042666 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042666

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042666/0 /scratch/stefan/7769623/working/building/REAL300000042666 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/734
`/scratch/stefan/7769623/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=CC(Br)=CC=C3O2)=C1)

`REAL300000042666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042666 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC(Br)=CC=C3O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 11, 35, 45, 45, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042666 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC(Br)=CC=C3O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 44, 45, 45, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 44, 45, 45, 35, 6, 1, 1, 1, 1, 45] 45
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042666 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042666
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042666/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042666
Building REAL300000042667
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042667'
/scratch/stefan/7769623/working/building/REAL300000042667 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042667

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042667/0 /scratch/stefan/7769623/working/building/REAL300000042667 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/735
`/scratch/stefan/7769623/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1=CC=C(C(C)C(C)N=NC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042667 none CC(C)CC1=CC=C(C(C)C(C)N=NC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 1, 1, 1, 1, 1, 9, 9, 29, 31, 119, 119, 185, 185, 185, 185, 185, 185, 185, 185, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 9, 9, 9, 9, 31, 31, 31, 31, 185, 185, 185, 185, 1, 1] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 48, 49, 35, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 370
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042667 none CC(C)CC1=CC=C(C(C)C(C)N=NC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 174, 169, 185, 185, 111, 40, 109, 7, 40, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 111, 111, 111, 111, 40, 40, 40, 40, 1, 1, 1, 1, 185, 185] 201
rigid atoms, others: [45, 44, 13, 14, 15, 16, 17, 18, 19, 46, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49])
total number of confs: 776
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042667 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042667
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042667/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042667
Building REAL300000042668
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042668'
/scratch/stefan/7769623/working/building/REAL300000042668 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042668

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042668/0 /scratch/stefan/7769623/working/building/REAL300000042668 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/736
`/scratch/stefan/7769623/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C2OC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC2=CC=C1)

`REAL300000042668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042668 none CCC1=C2OC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [4, 1, 1, 1, 1, 1, 1, 6, 6, 28, 44, 44, 44, 44, 44, 44, 44, 43, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 27, 44, 44, 44, 43, 1, 1, 1, 1] 84
rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 22, 36, 37, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042668 none CCC1=C2OC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [84, 44, 43, 43, 43, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 43, 43, 84, 84, 84, 84, 84, 33, 8, 1, 1, 1, 1, 43, 43, 43, 43] 84
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042668 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042668
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042668/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042668
Building REAL300000042669
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042669'
/scratch/stefan/7769623/working/building/REAL300000042669 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042669

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042669/0 /scratch/stefan/7769623/working/building/REAL300000042669 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/737
`/scratch/stefan/7769623/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)C=NC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042669 none CC1=C(Br)C=NC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 41, 54, 54, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1, 1, 13, 41, 54, 54, 54, 54] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042669 none CC1=C(Br)C=NC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 54, 54, 54, 54, 42, 12, 1, 1, 1, 1] 54
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042669 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042669
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042669/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042669
Building REAL300000042670
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042670'
/scratch/stefan/7769623/working/building/REAL300000042670 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042670

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042670/0 /scratch/stefan/7769623/working/building/REAL300000042670 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/738
`/scratch/stefan/7769623/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042670 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 11, 11, 66, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 1, 7, 7, 7, 1, 1, 11, 66, 159, 159, 159, 159, 1] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042670 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 201, 158, 159, 159, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 159, 159, 159, 201, 201, 201, 159, 159, 60, 12, 1, 1, 1, 1, 159] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 403
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042670 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042670
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042670/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042670
Building REAL300000042671
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042671'
/scratch/stefan/7769623/working/building/REAL300000042671 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042671

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042671/0 /scratch/stefan/7769623/working/building/REAL300000042671 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/739
`/scratch/stefan/7769623/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3CC3)=C2F)=C1)

`REAL300000042671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042671 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3CC3)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49, 85, 85, 85, 85, 85, 186, 201, 201, 85, 85, 1, 1, 1, 1, 10, 49, 85, 85, 85, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 345
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: REAL300000042671 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3CC3)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 169, 89, 89, 45, 45, 45, 45, 45, 10, 1, 1, 1, 1, 45, 45, 201, 201, 201, 201, 169, 89, 45, 45, 45, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 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, 30, 36])
total number of confs: 472
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042671 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3CC3)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 85, 84, 85, 85, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 12, 45, 45, 1, 1, 85, 84, 85, 85, 34, 6, 1, 1, 1, 45, 45, 45, 45, 45, 85] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 251
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042671 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042671
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042671/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042671
Building REAL300000042672
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042672'
/scratch/stefan/7769623/working/building/REAL300000042672 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042672

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042672/0 /scratch/stefan/7769623/working/building/REAL300000042672 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/740
`/scratch/stefan/7769623/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OC(F)F)=C1)

`REAL300000042672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042672 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 41, 41, 65, 65, 65, 65, 65, 65, 65, 129, 144, 144, 1, 1, 1, 1, 11, 41, 65, 65, 65, 144, 1] 144
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 297
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042672 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 37, 37, 65, 65, 65, 65, 24, 5, 1, 1, 1, 37, 65] 144
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042672 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042672
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042672/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042672
Building REAL300000042673
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042673'
/scratch/stefan/7769623/working/building/REAL300000042673 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042673

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042673/0 /scratch/stefan/7769623/working/building/REAL300000042673 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/741
`/scratch/stefan/7769623/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CN(C(F)F)C2=O)=C1)

`REAL300000042673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042673 none O=C([O-])C1=CC=CC(NN=CC2=CC=CN(C(F)F)C2=O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 15, 15, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 11, 51, 51, 70, 70, 70, 70, 70, 73, 73, 70, 70, 1, 1, 1, 1, 11, 51, 70, 70, 70, 73, 1] 73
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042673 none O=C([O-])C1=CC=CC(NN=CC2=CC=CN(C(F)F)C2=O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 15, 15, 1, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [70, 70, 70, 70, 69, 70, 70, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 70, 69, 70, 70, 33, 5, 1, 1, 1, 7, 70] 73
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042673 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042673
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042673/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042673
Building REAL300000042674
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042674'
/scratch/stefan/7769623/working/building/REAL300000042674 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042674

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042674/0 /scratch/stefan/7769623/working/building/REAL300000042674 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/742
`/scratch/stefan/7769623/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)=C1)

`REAL300000042674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042674 none O=C([O-])C1=CC=CC(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 66, 66, 66, 66, 66, 66, 66, 66, 25, 25, 1, 1, 1, 1, 25, 25, 25, 25, 25, 66, 66, 66, 25, 25, 25, 25, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042674 none O=C([O-])C1=CC=CC(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 45, 45, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 66, 66, 66, 66, 10, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 66] 66
rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41])
total number of confs: 89
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042674 none O=C([O-])C1=CC=CC(N=NC2CCN(C3=CC=C([N+](=O)[O-])N=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 8, 1, 1, 1, 1, 8, 11, 11, 8, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 25, 25, 25, 25, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 1, 1, 25] 66
rigid atoms, others: [32, 33, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 23, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 34, 35, 36, 41])
total number of confs: 43
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042674 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042674
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042674/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042674
Building REAL300000042675
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042675'
/scratch/stefan/7769623/working/building/REAL300000042675 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042675

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042675/0 /scratch/stefan/7769623/working/building/REAL300000042675 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/743
`/scratch/stefan/7769623/working/3D/743' -> `0.mol2'
Preparing input files

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

`REAL300000042675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042675 none O=C([O-])C1=CC=CC(N=NC(CCC(F)(F)F)CCC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 59, 115, 130, 130, 130, 130, 59, 117, 133, 133, 133, 133, 1, 1, 1, 1, 59, 125, 125, 130, 126, 127, 127, 128, 133, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 36] set([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: 938
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042675 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042675
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042675/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042675
Building REAL300000042676
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042676'
/scratch/stefan/7769623/working/building/REAL300000042676 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042676

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042676/0 /scratch/stefan/7769623/working/building/REAL300000042676 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/744
`/scratch/stefan/7769623/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC(F)F)=C1)

`REAL300000042676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042676 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 76, 76, 76, 44, 76, 76, 76, 170, 200, 200, 1, 1, 1, 1, 10, 43, 76, 43, 76, 200, 1] 200
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 519
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042676 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
200  conformations in input
total number of sets (complete confs): 200
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 76, 76, 76, 76, 28, 6, 1, 1, 1, 47, 76] 200
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 275
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042676 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042676
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042676/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042676
Building REAL300000042677
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042677'
/scratch/stefan/7769623/working/building/REAL300000042677 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042677

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042677/0 /scratch/stefan/7769623/working/building/REAL300000042677 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/745
`/scratch/stefan/7769623/working/3D/745' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC1=CC=C(Cl)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042677 none CCC(CC1=CC=C(Cl)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [18, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 53, 53, 124, 124, 124, 124, 124, 124, 124, 124, 18, 19, 19, 18, 19, 10, 3, 3, 1, 1, 1, 1, 124, 124, 124, 124] 126
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 239
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042677 none CCC(CC1=CC=C(Cl)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [69, 55, 8, 55, 110, 124, 124, 124, 124, 124, 124, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 85, 85, 85, 85, 55, 110, 110, 124, 124, 124, 124, 1, 1, 1, 1] 126
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 721
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042677 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042677
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042677/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042677
Building REAL300000042678
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042678'
/scratch/stefan/7769623/working/building/REAL300000042678 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042678

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042678/0 /scratch/stefan/7769623/working/building/REAL300000042678 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/746
`/scratch/stefan/7769623/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1)

`REAL300000042678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042678 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 63, 63, 25, 39, 147, 201, 201, 201, 201, 201, 201, 201, 63, 63, 23, 23, 23, 4, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 63] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 641
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: REAL300000042678 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 9, 61, 69, 167, 201, 201, 201, 201, 201, 201, 201, 201, 9, 31, 31, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 31, 62, 63, 64, 167, 201, 201, 201, 201, 31, 31, 3, 3, 3, 3, 1, 1, 1, 1, 1, 31, 31] 201
rigid atoms, others: [42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48])
total number of confs: 580
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042678 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC(C)C2=CC=CC=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 28, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 11, 24, 24, 31, 31, 31, 31, 31, 1, 1, 6, 6, 6, 28, 63, 63, 63, 63, 1, 1, 24, 24, 24, 24, 31, 31, 30, 31, 31, 1, 1] 201
rigid atoms, others: [1, 36, 37, 48, 47, 13, 14, 15, 16, 17, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 204
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042678 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042678
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042678/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042678
Building REAL300000042679
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042679'
/scratch/stefan/7769623/working/building/REAL300000042679 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042679

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042679/0 /scratch/stefan/7769623/working/building/REAL300000042679 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/747
`/scratch/stefan/7769623/working/3D/747' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=CC(Br)=C1)

`REAL300000042679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042679 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 106, 106, 106, 106, 106, 106, 41, 41, 41, 10, 1, 1, 1, 1, 106, 106, 106] 106
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30])
total number of confs: 161
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042679 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN=CC(Br)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [11, 1, 11, 11, 63, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 106, 106, 106, 106, 1, 1, 1] 106
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 229
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042679 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042679
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042679/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042679
Building REAL300000042680
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042680'
/scratch/stefan/7769623/working/building/REAL300000042680 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300000042680 as failed and skipping
/scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `/scratch/stefan/7769623/failed'
`/scratch/stefan/7769623/working/building/REAL300000042680' -> `/scratch/stefan/7769623/failed/REAL300000042680'
Building REAL300000042681
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042681'
/scratch/stefan/7769623/working/building/REAL300000042681 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042681

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042681/0 /scratch/stefan/7769623/working/building/REAL300000042681 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/748
`/scratch/stefan/7769623/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)=CC=C1)

`REAL300000042681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042681 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 7, 9, 9, 9, 1, 1, 1] 9
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042681 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC([O-])=C(Cl)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 6, 1, 1, 1, 9, 9, 9] 9
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042681 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042681/1 /scratch/stefan/7769623/working/building/REAL300000042681 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/749
`/scratch/stefan/7769623/working/3D/749' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)=CC=C1)

`REAL300000042681.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042681/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042681 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 1, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [2, 1, 2, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 12, 20, 20, 40, 20, 1, 1, 1] 42
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042681 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(O)=C(Cl)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 12, 1, 16, 1, 1, 1, 1, 1, 7, 6, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [21, 20, 21, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 7, 1, 1, 2, 1, 20, 20, 20] 42
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 28] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 27, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042681 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042681
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042681/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042681/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042681
Building REAL300000042682
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042682'
/scratch/stefan/7769623/working/building/REAL300000042682 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042682

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042682/0 /scratch/stefan/7769623/working/building/REAL300000042682 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/750
`/scratch/stefan/7769623/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3CCCC3)=C2)=C1)

`REAL300000042682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042682 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3CCCC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 53, 53, 117, 117, 103, 117, 117, 160, 160, 160, 160, 117, 1, 1, 1, 1, 13, 53, 117, 117, 103, 160, 160, 160, 160, 160, 160, 160, 160, 160, 117, 1] 160
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 386
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: REAL300000042682 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3CCCC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [160, 160, 160, 160, 160, 160, 160, 106, 30, 30, 6, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 6, 160, 160, 160, 160, 106, 30, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 160] 160
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 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, 40, 41])
total number of confs: 342
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042682 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3CCCC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [117, 117, 117, 117, 116, 117, 117, 63, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 117, 116, 117, 117, 63, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 117] 160
rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41])
total number of confs: 249
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042682 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042682
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042682/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042682
Building REAL300000042683
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042683'
/scratch/stefan/7769623/working/building/REAL300000042683 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042683

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042683/0 /scratch/stefan/7769623/working/building/REAL300000042683 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/751
`/scratch/stefan/7769623/working/3D/751' -> `0.mol2'
Preparing input files

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

`REAL300000042683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042683 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 32, 32, 50, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 6, 32, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042683 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 51, 51, 51, 51, 43, 9, 9, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 51, 51, 51, 51, 43, 9, 1, 1, 1, 51] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042683 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042683
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042683/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042683
Building REAL300000042684
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042684'
/scratch/stefan/7769623/working/building/REAL300000042684 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042684

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042684/0 /scratch/stefan/7769623/working/building/REAL300000042684 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/752
`/scratch/stefan/7769623/working/3D/752' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F)

`REAL300000042684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042684 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 9, 9, 52, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1, 1, 13, 13, 13, 1, 1, 9, 52, 118, 118, 118, 118, 1] 184
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042684 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 117, 184, 117, 118, 118, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 118, 118, 118, 184, 184, 184, 118, 118, 53, 12, 1, 1, 1, 1, 118] 184
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 420
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042684 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042684
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042684/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042684
Building REAL300000042685
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042685'
/scratch/stefan/7769623/working/building/REAL300000042685 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042685

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042685/0 /scratch/stefan/7769623/working/building/REAL300000042685 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/753
`/scratch/stefan/7769623/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1)

`REAL300000042685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042685 none CN1C=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 61, 61, 146, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 2, 2, 2, 1, 12, 12, 12, 12, 61, 146, 172, 172, 172, 172, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 38, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 421
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042685 none CN1C=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [172, 172, 172, 111, 111, 111, 111, 111, 111, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 172, 172, 172, 172, 172, 172, 111, 111, 111, 111, 38, 9, 1, 1, 1, 1, 172] 172
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 268
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042685 none CN1C=C(C2=NN(C)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 56, 111, 111, 111, 111, 111, 111, 111, 111, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 12, 56, 111, 111, 111, 111, 12] 172
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 235
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042685 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042685
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042685/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042685
Building REAL300000042686
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042686'
/scratch/stefan/7769623/working/building/REAL300000042686 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042686

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042686/0 /scratch/stefan/7769623/working/building/REAL300000042686 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/754
`/scratch/stefan/7769623/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042686 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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, 23, 10, 1, 1, 1, 1, 1, 1, 4, 4, 16, 36, 36, 36, 36, 36, 37, 37, 36, 1, 10, 10, 1, 1, 4, 16, 36, 36, 36, 36] 67
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042686 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [66, 67, 67, 67, 36, 36, 36, 36, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 67, 67, 36, 36, 26, 6, 1, 1, 1, 1] 67
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 167
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042686 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042686/1 /scratch/stefan/7769623/working/building/REAL300000042686 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/755
`/scratch/stefan/7769623/working/3D/755' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042686.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042686/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042686 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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: [5, 4, 6, 4, 1, 1, 1, 1, 1, 1, 5, 19, 19, 25, 25, 25, 25, 25, 25, 25, 25, 1, 4, 4, 1, 1, 5, 5, 25, 25, 25, 25] 25
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042686 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 25, 25, 18, 18, 1, 1, 1, 1] 25
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042686 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042686
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042686/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042686/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042686
Building REAL300000042687
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042687'
/scratch/stefan/7769623/working/building/REAL300000042687 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042687

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042687/0 /scratch/stefan/7769623/working/building/REAL300000042687 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/756
`/scratch/stefan/7769623/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C1)

`REAL300000042687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042687 none CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 14, 17, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 90, 90, 90, 89, 89, 90, 90, 89, 1, 1, 1, 18, 18, 18, 17, 17, 17, 18, 18, 18, 1, 1, 1, 1, 1, 1, 8, 42, 90, 90, 90, 89, 1, 1, 1] 201
rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 13, 14, 40, 50, 51, 52, 43, 41, 26, 27, 28, 42] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042687 none CC(C)(C)OC(=O)N1CCC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 148, 89, 147, 89, 89, 89, 89, 89, 89, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 89, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 89, 35, 8, 1, 1, 1, 1, 89, 89, 89] 201
rigid atoms, others: [48, 49, 46, 47, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52])
total number of confs: 445
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042687 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042687
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042687/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042687
Building REAL300000042688
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042688'
/scratch/stefan/7769623/working/building/REAL300000042688 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042688

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042688/0 /scratch/stefan/7769623/working/building/REAL300000042688 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/757
`/scratch/stefan/7769623/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=C1)

`REAL300000042688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042688 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 85, 85, 85, 85, 200, 201, 201, 201, 201, 201, 201, 85, 85, 1, 1, 1, 1, 9, 33, 85, 85, 201, 201, 201, 201, 85, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042688 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 153, 68, 68, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 201, 201, 201, 201, 153, 68, 18, 18, 1, 1, 1, 1, 18, 201] 201
rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 481
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042688 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3=CC=C(F)C=C3)N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 85, 84, 85, 85, 44, 8, 8, 1, 1, 1, 1, 1, 1, 8, 18, 18, 10, 18, 18, 18, 1, 1, 85, 84, 85, 85, 44, 8, 1, 1, 18, 18, 18, 18, 1, 85] 201
rigid atoms, others: [32, 37, 10, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 38])
total number of confs: 219
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042688 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042688
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042688/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042688
Building REAL300000042689
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042689'
/scratch/stefan/7769623/working/building/REAL300000042689 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042689

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042689/0 /scratch/stefan/7769623/working/building/REAL300000042689 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/758
`/scratch/stefan/7769623/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=C1)

`REAL300000042689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042689 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 13, 67, 67, 142, 142, 142, 142, 171, 171, 171, 171, 171, 171, 142, 1, 1, 1, 1, 13, 67, 142, 171, 171, 171, 171, 1] 171
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 271
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042689 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 171, 171, 171, 120, 25, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 171, 171, 171, 171, 120, 25, 5, 1, 1, 1, 1, 171] 171
rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 372
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042689 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(C3=CC=CC(Cl)=C3)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [142, 142, 142, 142, 142, 142, 142, 55, 10, 10, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 142, 142, 142, 142, 54, 10, 1, 5, 5, 4, 5, 142] 171
rigid atoms, others: [10, 11, 12, 13, 14, 15, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 255
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042689 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042689
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042689/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042689
Building REAL300000042690
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042690'
/scratch/stefan/7769623/working/building/REAL300000042690 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042690

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042690/0 /scratch/stefan/7769623/working/building/REAL300000042690 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/759
`/scratch/stefan/7769623/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=NC=C2S1)

`REAL300000042690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042690 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 66, 66, 66, 66, 66, 66, 66, 66, 41, 41, 41, 10, 1, 1, 1, 1, 66, 67, 66, 66] 67
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 117
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042690 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 40, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 39, 67, 67, 67, 66, 1, 1, 1, 1] 67
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 149
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042690 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042690
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042690/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042690
Building REAL300000042691
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042691'
/scratch/stefan/7769623/working/building/REAL300000042691 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042691

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042691/0 /scratch/stefan/7769623/working/building/REAL300000042691 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/760
`/scratch/stefan/7769623/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1)

`REAL300000042691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042691 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 55, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042691 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 36, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 36, 36, 36, 36, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 4] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 345
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042691 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 13, 13, 13, 13, 201, 201, 201, 201, 2, 2, 2, 4, 4, 2, 4, 4, 1] 201
rigid atoms, others: [1, 41, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042691 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042691/1 /scratch/stefan/7769623/working/building/REAL300000042691 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/761
`/scratch/stefan/7769623/working/3D/761' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1)

`REAL300000042691.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042691/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042691 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 60, 60, 60, 60, 60, 61, 61, 60, 61, 61, 60, 43, 43, 43, 10, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 60] 61
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 113
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042691 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [18, 4, 18, 18, 54, 61, 61, 61, 61, 61, 61, 61, 61, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 18, 54, 61, 61, 61, 61, 4, 4, 4, 1, 1, 1, 1, 1, 4] 61
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 145
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042691 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=NN(C)C(C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 33, 60, 60, 60, 60, 60, 61, 61, 60, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 10, 10, 10, 33, 60, 60, 60, 60, 2, 2, 2, 4, 4, 3, 4, 4, 1] 61
rigid atoms, others: [1, 41, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: 153
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042691 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042691
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042691/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042691/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042691
Building REAL300000042692
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042692'
/scratch/stefan/7769623/working/building/REAL300000042692 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042692

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042692/0 /scratch/stefan/7769623/working/building/REAL300000042692 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/762
`/scratch/stefan/7769623/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CSC(C(F)(F)F)=C2)=C1)

`REAL300000042692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042692 none O=C([O-])C1=CC=CC(NN=CC2=CSC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 48, 48, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 12, 48, 78, 78, 1] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042692 none O=C([O-])C1=CC=CC(NN=CC2=CSC(C(F)(F)F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 77, 78, 78, 48, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 78, 77, 78, 78, 48, 10, 1, 1, 78] 78
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042692 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042692
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042692/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042692
Building REAL300000042693
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042693'
/scratch/stefan/7769623/working/building/REAL300000042693 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042693

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042693/0 /scratch/stefan/7769623/working/building/REAL300000042693 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/763
`/scratch/stefan/7769623/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C(F)(F)F)SC=C2)=C1)

`REAL300000042693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042693 none O=C([O-])C1=CC=CC(NN=CC2=C(C(F)(F)F)SC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 45, 45, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 13, 45, 65, 65, 1] 65
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042693 none O=C([O-])C1=CC=CC(NN=CC2=C(C(F)(F)F)SC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 65, 65, 65, 65, 65, 40, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 65, 65, 65, 65, 40, 9, 1, 1, 65] 65
rigid atoms, others: [10, 11, 12, 13, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 141
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042693 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042693
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042693/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042693
Building REAL300000042694
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042694'
/scratch/stefan/7769623/working/building/REAL300000042694 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042694

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042694/0 /scratch/stefan/7769623/working/building/REAL300000042694 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/764
`/scratch/stefan/7769623/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2CCOCC2)=C1)

`REAL300000042694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042694 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2CCOCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 60, 60, 131, 131, 131, 131, 131, 159, 159, 159, 159, 159, 1, 1, 1, 1, 13, 60, 131, 131, 159, 159, 159, 159, 159, 159, 159, 159, 159, 1] 159
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 309
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042694 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2CCOCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 159, 159, 159, 159, 113, 31, 31, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 113, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159] 159
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 39])
total number of confs: 356
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042694 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2CCOCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 60, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 131, 131, 131, 131, 60, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 131] 159
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042694 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042694
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042694/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042694
Building REAL300000042695
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042695'
/scratch/stefan/7769623/working/building/REAL300000042695 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042695

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042695/0 /scratch/stefan/7769623/working/building/REAL300000042695 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/765
`/scratch/stefan/7769623/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC=C3)CC2)=C1)

`REAL300000042695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042695 none O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042695 none O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 18, 18, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 28, 28, 28, 28, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 28] 28
rigid atoms, others: [35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44])
total number of confs: 41
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042695 none O=C([O-])C1=CC=CC(N=NC2CCCC(C3=CC=CC=C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 28] 28
rigid atoms, others: [32, 33, 34, 43, 40, 9, 10, 11, 12, 13, 14, 15, 42, 21, 22, 41, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 23, 24, 25, 26, 35, 36, 37, 38, 39, 44])
total number of confs: 44
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042695 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042695
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042695/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042695
Building REAL300000042696
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042696'
/scratch/stefan/7769623/working/building/REAL300000042696 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042696

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042696/0 /scratch/stefan/7769623/working/building/REAL300000042696 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/766
`/scratch/stefan/7769623/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=CC(F)=C1F)

`REAL300000042696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042696 none CN(C)C1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=CC(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 5, 5, 22, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 5, 22, 35, 35, 35, 35, 1, 1] 35
rigid atoms, others: [19, 1, 3, 4, 5, 17, 18, 35, 20, 21, 22, 36] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 80
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042696 none CN(C)C1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=CC(F)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 35, 34, 34, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 34, 11, 1, 1, 1, 1, 35, 35] 35
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 62
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042696 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042696
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042696/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042696
Building REAL300000042697
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042697'
/scratch/stefan/7769623/working/building/REAL300000042697 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042697

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042697/0 /scratch/stefan/7769623/working/building/REAL300000042697 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/767
`/scratch/stefan/7769623/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=CC=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C=C1OC)

`REAL300000042697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042697 none COC1=CC2=CC=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 77, 155, 155, 155, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 3, 4, 4, 4, 1, 1, 1, 13, 13, 13, 77, 155, 155, 155, 155, 1, 1, 3, 3, 3] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 21, 22, 23, 24, 25, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45])
total number of confs: 324
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042697 none COC1=CC2=CC=C(C(C)=NNC3=CC=CC(C(=O)[O-])=C3)C=C2C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 155, 155, 155, 155, 155, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 155, 155, 155, 155, 155, 201, 201, 201, 201, 155, 155, 155, 36, 36, 36, 8, 1, 1, 1, 1, 155, 155, 201, 201, 201] 201
rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45])
total number of confs: 397
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042697 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042697
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042697/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042697
Building REAL300000042698
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042698'
/scratch/stefan/7769623/working/building/REAL300000042698 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042698

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042698/0 /scratch/stefan/7769623/working/building/REAL300000042698 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/768
`/scratch/stefan/7769623/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042698 none CC1=CC(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 2, 1, 2, 8, 28, 39, 39, 39, 39, 1] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 97
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042698 none CC1=CC(O)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [39, 37, 39, 39, 39, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 39, 39, 39, 39, 39, 78, 31, 11, 1, 1, 1, 1, 39] 78
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 158
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042698 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042698
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042698/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042698
Building REAL300000042699
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042699'
/scratch/stefan/7769623/working/building/REAL300000042699 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042699

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042699/0 /scratch/stefan/7769623/working/building/REAL300000042699 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/769
`/scratch/stefan/7769623/working/3D/769' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(F)=C2Cl)=C1)

`REAL300000042699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042699 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(F)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 38, 38, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 13, 38, 68, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042699 none O=C([O-])C1=CC=CC(NN=CC2=C(F)C=CC(F)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 50, 12, 1, 1, 68] 68
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042699 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042699
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042699/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042699
Building REAL300000042700
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042700'
/scratch/stefan/7769623/working/building/REAL300000042700 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042700

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042700/0 /scratch/stefan/7769623/working/building/REAL300000042700 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/770
`/scratch/stefan/7769623/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC(F)=C(Cl)C=C32)=C1)

`REAL300000042700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042700 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(F)=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 31
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042700 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC(F)=C(Cl)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 17] 17
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 21, 22, 23, 24, 25])
total number of confs: 29
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042700 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042700
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042700/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042700
Building REAL300000042701
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042701'
/scratch/stefan/7769623/working/building/REAL300000042701 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042701

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042701/0 /scratch/stefan/7769623/working/building/REAL300000042701 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/771
`/scratch/stefan/7769623/working/3D/771' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(CC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042701 none CCC1=CC=C(C(CC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 12, 33, 36, 36, 12, 12, 58, 119, 119, 119, 119, 119, 120, 120, 119, 1, 1, 4, 4, 4, 3, 3, 1, 1, 33, 33, 36, 36, 36, 36, 36, 36, 36, 58, 119, 119, 119, 119, 1, 1] 134
rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 46, 22, 23, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 371
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042701 none CCC1=CC=C(C(CC(C)C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [120, 39, 33, 119, 119, 33, 33, 33, 63, 67, 67, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 119, 119, 121, 121, 121, 120, 120, 119, 119, 63, 63, 67, 67, 67, 67, 67, 67, 67, 8, 1, 1, 1, 1, 119, 119] 134
rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
total number of confs: 825
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042701 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042701
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042701/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042701
Building REAL300000042702
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042702'
/scratch/stefan/7769623/working/building/REAL300000042702 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042702

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042702/0 /scratch/stefan/7769623/working/building/REAL300000042702 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/772
`/scratch/stefan/7769623/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042702 none CC(C)OC1=CC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 17, 1, 1, 1, 1, 1, 1, 1, 8, 8, 42, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 8, 42, 98, 98, 98, 98, 1] 155
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 38, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 228
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042702 none CC(C)OC1=CC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 155, 98, 63, 98, 98, 98, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 98, 98, 98, 155, 155, 155, 155, 155, 155, 155, 98, 50, 9, 1, 1, 1, 1, 98] 155
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 405
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042702 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042702
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042702/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042702
Building REAL300000042703
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042703'
/scratch/stefan/7769623/working/building/REAL300000042703 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042703

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042703/0 /scratch/stefan/7769623/working/building/REAL300000042703 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/773
`/scratch/stefan/7769623/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3CCOC3)C=C2)=C1)

`REAL300000042703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042703 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 62, 62, 43, 43, 140, 201, 201, 201, 201, 62, 62, 1, 1, 1, 1, 9, 43, 62, 62, 201, 201, 201, 201, 201, 201, 201, 62, 62, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
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: REAL300000042703 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 148, 67, 56, 17, 15, 33, 33, 7, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 148, 54, 33, 33, 1, 1, 1, 1, 1, 1, 1, 33, 33, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 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, 38, 39, 40])
total number of confs: 528
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042703 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC3CCOC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 62, 62, 62, 24, 4, 4, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 33, 1, 1, 62, 62, 62, 62, 24, 4, 1, 1, 33, 33, 33, 33, 33, 33, 33, 1, 1, 62] 201
rigid atoms, others: [38, 39, 10, 11, 12, 13, 14, 15, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 40])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042703 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042703
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042703/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042703
Building REAL300000042704
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042704'
/scratch/stefan/7769623/working/building/REAL300000042704 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042704

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042704/0 /scratch/stefan/7769623/working/building/REAL300000042704 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/774
`/scratch/stefan/7769623/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC(C)(C)C1)

`REAL300000042704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042704 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC(C)(C)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [15, 12, 15, 15, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 16, 16, 16, 15, 15, 15, 16, 16, 16, 1, 1, 1, 1, 1, 39, 39, 39, 39, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 101
rigid atoms, others: [11, 36, 5, 38, 7, 8, 9, 10, 39, 45, 46, 40, 53, 22, 23, 24, 25, 26, 54, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52])
total number of confs: 110
number of broken/clashed sets: 101
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042704 none CC(C)(C)OC(=O)N1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC(C)(C)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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 101, 65, 39, 65, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 39, 39, 39, 101, 101, 101, 101, 101, 101, 101, 101, 101, 39, 39, 39, 39, 39, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 101
rigid atoms, others: [41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 255
number of broken/clashed sets: 101
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042704 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042704
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042704/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042704
Building REAL300000042705
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042705'
/scratch/stefan/7769623/working/building/REAL300000042705 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042705

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042705/0 /scratch/stefan/7769623/working/building/REAL300000042705 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/775
`/scratch/stefan/7769623/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=C(O)C=CC=C3S2)=C1)

`REAL300000042705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042705 none O=C([O-])C1=CC=CC(NN=CC2=CC3=C(O)C=CC=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 33, 33, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 11, 33, 55, 110, 55, 55, 55, 1] 110
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 204
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042705 none O=C([O-])C1=CC=CC(NN=CC2=CC3=C(O)C=CC=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 42, 9, 1, 2, 1, 1, 1, 55] 110
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 21, 22, 23, 24, 25, 26, 28])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042705 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042705
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042705/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042705
Building REAL300000042706
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042706'
/scratch/stefan/7769623/working/building/REAL300000042706 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042706

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042706/0 /scratch/stefan/7769623/working/building/REAL300000042706 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/776
`/scratch/stefan/7769623/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F)

`REAL300000042706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042706 none CN(C)C1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 27, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 9, 27, 30, 30, 30, 30, 1] 30
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 36, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042706 none CN(C)C1=CC(F)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 28, 30, 30, 30, 30, 30, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 21, 7, 1, 1, 1, 1, 30] 30
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042706 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042706
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042706/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042706
Building REAL300000042707
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042707'
/scratch/stefan/7769623/working/building/REAL300000042707 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042707

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042707/0 /scratch/stefan/7769623/working/building/REAL300000042707 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/777
`/scratch/stefan/7769623/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=C(Br)C=C1F)

`REAL300000042707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042707 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 83, 83, 83, 83, 83, 83, 83, 83, 40, 40, 40, 10, 1, 1, 1, 1, 83, 83] 83
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 141
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042707 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 17, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 53, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 83, 83, 83, 83, 1, 1] 83
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 181
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042707 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042707
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042707/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042707
Building REAL300000042708
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042708'
/scratch/stefan/7769623/working/building/REAL300000042708 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042708

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042708/0 /scratch/stefan/7769623/working/building/REAL300000042708 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/778
`/scratch/stefan/7769623/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=NC=C2)=C1)

`REAL300000042708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042708 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=NC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 153, 153, 153, 153, 153, 157, 157, 157, 157, 157, 1, 1, 1, 1, 13, 67, 153, 153, 157, 157, 157, 157, 1] 157
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 221
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: REAL300000042708 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=NC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 157, 157, 157, 157, 104, 24, 24, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 104, 24, 5, 5, 1, 1, 1, 1, 157] 157
rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 335
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042708 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=NC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 153, 153, 153, 153, 153, 80, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 153, 153, 153, 153, 80, 12, 1, 1, 5, 5, 5, 5, 153] 157
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34])
total number of confs: 311
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042708 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042708/1 /scratch/stefan/7769623/working/building/REAL300000042708 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/779
`/scratch/stefan/7769623/working/3D/779' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)=C1)

`REAL300000042708.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042708/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042708 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 1] 6
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 13
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042708 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 6] 6
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 13
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042708 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2C2=CC=[NH+]C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 3, 4, 4, 6, 6, 6, 6, 4, 4, 1, 1, 4, 4, 4, 4, 6] 6
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 24
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042708 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042708
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042708/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042708/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042708
Building REAL300000042709
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042709'
/scratch/stefan/7769623/working/building/REAL300000042709 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042709

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042709/0 /scratch/stefan/7769623/working/building/REAL300000042709 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/780
`/scratch/stefan/7769623/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+](CC2=CC=CC=C2)C1)

`REAL300000042709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042709 none CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 4, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 5, 9, 9, 5, 9, 9, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 1, 1] 29
rigid atoms, others: [1, 4, 5, 44, 45, 46, 47, 17, 18, 19, 20, 21, 55, 56, 28] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 77
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042709 none CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 29, 29, 29, 29, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9] 29
rigid atoms, others: [54, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56])
total number of confs: 87
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042709 none CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 20, 20] 29
rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 108
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042709 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042709/1 /scratch/stefan/7769623/working/building/REAL300000042709 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/781
`/scratch/stefan/7769623/working/3D/781' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+](CC2=CC=CC=C2)C1)

`REAL300000042709.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042709/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042709 none CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 4, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 5, 9, 9, 7, 9, 9, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 9, 9, 7, 9, 9, 1, 1] 29
rigid atoms, others: [1, 4, 5, 44, 45, 46, 47, 17, 18, 19, 20, 21, 55, 56, 28] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 71
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042709 none CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 29, 29, 29, 29, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 9, 9] 29
rigid atoms, others: [54, 50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 55, 56])
total number of confs: 87
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042709 none CC(C)(C)C1(CN=NC2=CC=CC(C(=O)[O-])=C2)CC[N@@H+](CC2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 20, 20] 29
rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56])
total number of confs: 108
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042709 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042709
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042709/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042709/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042709
Building REAL300000042710
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042710'
/scratch/stefan/7769623/working/building/REAL300000042710 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042710

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042710/0 /scratch/stefan/7769623/working/building/REAL300000042710 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/782
`/scratch/stefan/7769623/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)F)N=C1)

`REAL300000042710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042710 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 147, 147, 147, 147, 180, 180, 147, 147, 47, 47, 47, 10, 1, 1, 1, 1, 147, 147, 180, 147] 180
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 411
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042710 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)F)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 59, 147, 147, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 12, 12, 1, 1, 11, 11, 11, 59, 147, 147, 147, 147, 1, 1, 12, 1] 180
rigid atoms, others: [1, 33, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 306
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042710 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042710
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042710/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042710
Building REAL300000042711
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042711'
/scratch/stefan/7769623/working/building/REAL300000042711 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042711

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042711/0 /scratch/stefan/7769623/working/building/REAL300000042711 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/783
`/scratch/stefan/7769623/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CC=C2C1)

`REAL300000042711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042711 none CC(C)(C)OC(=O)N1CCC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CC=C2C1 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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 48, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 23, 23, 23, 22, 22, 22, 23, 23, 23, 1, 1, 1, 1, 11, 48, 86, 86, 86, 86, 1, 1, 1, 1, 1] 201
rigid atoms, others: [11, 5, 38, 7, 8, 9, 10, 39, 12, 48, 40, 50, 51, 52, 49, 41, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042711 none CC(C)(C)OC(=O)N1CCC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CC=C2C1 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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 140, 86, 140, 86, 86, 86, 86, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 86, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 86, 38, 9, 1, 1, 1, 1, 86, 86, 86, 86, 86] 201
rigid atoms, others: [44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52])
total number of confs: 435
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042711 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042711
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042711/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042711
Building REAL300000042712
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042712'
/scratch/stefan/7769623/working/building/REAL300000042712 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042712

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042712/0 /scratch/stefan/7769623/working/building/REAL300000042712 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/784
`/scratch/stefan/7769623/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C2CCCCN2C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042712 none COC(=O)C1=C2CCCCN2C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 61, 61, 61, 61, 61, 62, 62, 61, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 61, 61, 61, 61, 1] 103
rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 42, 24, 28, 29, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 36, 37, 38, 39, 40, 41])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042712 none COC(=O)C1=C2CCCCN2C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [102, 102, 61, 102, 60, 61, 61, 61, 61, 61, 61, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 103, 103, 103, 61, 61, 61, 61, 61, 61, 61, 61, 29, 6, 1, 1, 1, 1, 61] 103
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 268
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042712 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042712
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042712/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042712
Building REAL300000042713
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042713'
/scratch/stefan/7769623/working/building/REAL300000042713 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042713

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042713/0 /scratch/stefan/7769623/working/building/REAL300000042713 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/785
`/scratch/stefan/7769623/working/3D/785' -> `0.mol2'
Preparing input files

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

`REAL300000042713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042713 none CCC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [17, 9, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 51, 51, 125, 125, 125, 125, 125, 125, 125, 125, 17, 18, 18, 17, 18, 10, 4, 4, 1, 1, 1, 1, 125, 125, 125, 125] 125
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 12, 13, 35, 36] set([0, 1, 2, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 253
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042713 none CCC(CC1=CC=C(C(F)(F)F)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [61, 54, 8, 54, 112, 125, 125, 118, 125, 125, 125, 125, 125, 125, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 76, 76, 76, 76, 76, 54, 112, 112, 125, 125, 125, 125, 1, 1, 1, 1] 125
rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 721
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042713 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042713
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042713/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042713
Building REAL300000042714
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042714'
/scratch/stefan/7769623/working/building/REAL300000042714 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042714

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042714/0 /scratch/stefan/7769623/working/building/REAL300000042714 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/786
`/scratch/stefan/7769623/working/3D/786' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(I)C=C32)=C1)

`REAL300000042714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042714 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(I)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 18, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 28
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042714 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=C(I)C=C32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 18, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 15] 15
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24])
total number of confs: 26
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042714 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042714
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042714/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042714
Building REAL300000042715
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042715'
/scratch/stefan/7769623/working/building/REAL300000042715 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042715

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042715/0 /scratch/stefan/7769623/working/building/REAL300000042715 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/787
`/scratch/stefan/7769623/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(C(F)(F)F)=C1)

`REAL300000042715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042715 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 13, 13, 59, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 1, 13, 59, 134, 134, 134, 134, 1, 1] 139
rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 28, 29, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042715 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [139, 134, 134, 134, 56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 134, 134, 134, 134, 134, 134, 133, 139, 139, 139, 134, 56, 10, 1, 1, 1, 1, 134, 133] 139
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 212
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042715 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042715
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042715/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042715
Building REAL300000042716
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042716'
/scratch/stefan/7769623/working/building/REAL300000042716 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042716

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042716/0 /scratch/stefan/7769623/working/building/REAL300000042716 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/788
`/scratch/stefan/7769623/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOC1=C(Cl)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC)

`REAL300000042716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042716 none C=CCOC1=C(Cl)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 16, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 4, 37, 37, 37, 16, 16, 1, 6, 26, 56, 56, 56, 55, 1, 4, 4, 4] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 30, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042716 none C=CCOC1=C(Cl)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 193, 96, 55, 55, 55, 55, 55, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 56, 111, 201, 201, 201, 194, 193, 55, 24, 6, 1, 1, 1, 1, 56, 111, 111, 111] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 797
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042716 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042716
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042716/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042716
Building REAL300000042717
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042717'
/scratch/stefan/7769623/working/building/REAL300000042717 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042717

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042717/0 /scratch/stefan/7769623/working/building/REAL300000042717 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/789
`/scratch/stefan/7769623/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC1CC1)

`REAL300000042717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042717 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 55, 55, 55, 55, 55, 56, 56, 55, 1, 1, 1, 10, 36, 36, 4, 4, 4, 1, 1, 6, 24, 55, 55, 55, 55, 1, 36, 36, 36, 36, 36] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 200
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: REAL300000042717 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 36, 36, 36, 36, 36, 36, 95, 95, 165, 201, 201, 201, 201, 201, 201, 201, 201, 36, 8, 1, 1, 1, 1, 57, 57, 57, 36, 36, 95, 165, 201, 201, 201, 201, 36, 1, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 521
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042717 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 55, 55, 55, 55, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 55, 161, 201, 201, 107, 107, 107, 55, 55, 20, 4, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 488
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042717 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042717
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042717/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042717
Building REAL300000042718
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042718'
/scratch/stefan/7769623/working/building/REAL300000042718 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042718

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042718/0 /scratch/stefan/7769623/working/building/REAL300000042718 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/790
`/scratch/stefan/7769623/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C=C2O)=C1)

`REAL300000042718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042718 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 9, 29, 29, 29, 29, 58, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28])
total number of confs: 105
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042718 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [29, 29, 29, 29, 29, 29, 29, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 24, 6, 1, 1, 1, 2, 29] 58
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28, 29])
total number of confs: 71
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042718 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042718
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042718/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042718
Building REAL300000042719
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042719'
/scratch/stefan/7769623/working/building/REAL300000042719 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042719

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042719/0 /scratch/stefan/7769623/working/building/REAL300000042719 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/791
`/scratch/stefan/7769623/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(F)(F)F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042719 none CN1N=C(C(F)(F)F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 45, 70, 70, 70, 70, 70, 71, 71, 70, 2, 2, 2, 1, 10, 45, 70, 70, 70, 70] 71
rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 25] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042719 none CN1N=C(C(F)(F)F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 70, 70, 71, 71, 71, 70, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 71, 70, 52, 12, 1, 1, 1, 1] 71
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27])
total number of confs: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042719 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042719
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042719/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042719
Building REAL300000042720
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042720'
/scratch/stefan/7769623/working/building/REAL300000042720 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042720

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042720/0 /scratch/stefan/7769623/working/building/REAL300000042720 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/792
`/scratch/stefan/7769623/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042720 none COCC(C)OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 55, 18, 6, 18, 1, 1, 1, 1, 1, 1, 6, 6, 20, 33, 33, 33, 33, 33, 34, 34, 33, 1, 1, 88, 88, 88, 55, 55, 18, 18, 18, 18, 1, 1, 6, 20, 33, 33, 33, 33, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 340
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042720 none COCC(C)OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 85, 154, 34, 25, 34, 33, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 201, 201, 201, 201, 201, 154, 153, 154, 154, 34, 33, 14, 4, 1, 1, 1, 1, 34, 34] 201
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 796
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042720 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042720
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042720/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042720
Building REAL300000042721
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042721'
/scratch/stefan/7769623/working/building/REAL300000042721 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042721

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042721/0 /scratch/stefan/7769623/working/building/REAL300000042721 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/793
`/scratch/stefan/7769623/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)=C1)

`REAL300000042721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042721 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 38, 38, 23, 38, 38, 38, 77, 144, 201, 201, 144, 201, 201, 201, 201, 1, 1, 1, 1, 8, 22, 38, 38, 38, 38, 144, 144, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 823
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042721 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 196, 158, 158, 113, 113, 113, 113, 113, 113, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 196, 158, 113, 113, 113, 113, 8, 8, 1, 1, 1, 201] 201
rigid atoms, others: [39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42])
total number of confs: 488
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042721 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 113, 113, 33, 113, 113, 113, 113, 38, 38, 38, 38, 21, 7, 1, 1, 1, 1, 33, 33, 113, 113, 113, 38] 201
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 521
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042721 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042721
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042721/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042721
Building REAL300000042722
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042722'
/scratch/stefan/7769623/working/building/REAL300000042722 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042722

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042722/0 /scratch/stefan/7769623/working/building/REAL300000042722 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/794
`/scratch/stefan/7769623/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CS3)C=C2)=C1)

`REAL300000042722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042722 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CS3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 49, 49, 56, 56, 51, 56, 151, 151, 151, 151, 56, 56, 1, 1, 1, 1, 13, 49, 56, 56, 151, 151, 151, 56, 56, 1] 151
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 247
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042722 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CS3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 151, 151, 151, 151, 151, 122, 40, 35, 2, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 151, 151, 151, 151, 122, 19, 12, 12, 1, 1, 1, 12, 12, 151] 151
rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 358
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042722 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CS3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [56, 56, 56, 56, 56, 56, 56, 27, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 56, 56, 56, 56, 26, 5, 1, 1, 12, 12, 12, 1, 1, 56] 151
rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35])
total number of confs: 114
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042722 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042722
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042722/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042722
Building REAL300000042723
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042723'
/scratch/stefan/7769623/working/building/REAL300000042723 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042723

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042723/0 /scratch/stefan/7769623/working/building/REAL300000042723 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/795
`/scratch/stefan/7769623/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Br)

`REAL300000042723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042723 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 65, 65, 65, 65, 65, 65, 65, 65, 65, 45, 45, 45, 12, 1, 1, 1, 1, 65, 65, 65] 65
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 118
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042723 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 7, 31, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 31, 65, 65, 65, 65, 1, 1, 1] 65
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 129
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042723 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042723
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042723/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042723
Building REAL300000042724
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042724'
/scratch/stefan/7769623/working/building/REAL300000042724 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042724

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042724/0 /scratch/stefan/7769623/working/building/REAL300000042724 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/796
`/scratch/stefan/7769623/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NN2CCC2=CC=CC=C2)=C1)

`REAL300000042724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042724 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2CCC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 117, 117, 117, 117, 117, 184, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 13, 50, 117, 117, 184, 184, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042724 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2CCC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 165, 58, 58, 15, 15, 15, 15, 15, 5, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 165, 58, 15, 15, 5, 5, 3, 3, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41])
total number of confs: 497
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042724 none O=C([O-])C1=CC=CC(NN=CC2=CC=NN2CCC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [117, 117, 117, 117, 117, 117, 117, 59, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 11, 15, 15, 11, 15, 15, 117, 117, 117, 117, 59, 8, 1, 1, 5, 5, 11, 11, 15, 15, 15, 15, 15, 117] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 292
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042724 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042724
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042724/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042724
Building REAL300000042725
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042725'
/scratch/stefan/7769623/working/building/REAL300000042725 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042725

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042725/0 /scratch/stefan/7769623/working/building/REAL300000042725 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/797
`/scratch/stefan/7769623/working/3D/797' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OCC(F)(F)F)=C1)

`REAL300000042725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042725 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OCC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 61, 61, 146, 146, 146, 146, 146, 146, 146, 172, 201, 201, 201, 201, 1, 1, 1, 1, 11, 61, 146, 146, 146, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 432
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042725 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OCC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 146, 146, 146, 54, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 146, 146, 146, 146, 54, 13, 1, 1, 1, 12, 12, 146] 201
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 289
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042725 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042725
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042725/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042725
Building REAL300000042726
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042726'
/scratch/stefan/7769623/working/building/REAL300000042726 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042726

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042726/0 /scratch/stefan/7769623/working/building/REAL300000042726 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/798
`/scratch/stefan/7769623/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=NOC=C1)

`REAL300000042726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042726 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 44, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 9, 9, 9, 9, 2, 2, 2, 1, 10, 44, 66, 66, 66, 66, 2, 2, 2, 9, 9] 107
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 157
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042726 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 42, 42, 91, 107, 107, 107, 107, 107, 107, 107, 107, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 42, 91, 107, 107, 107, 107, 9, 9, 9, 1, 1] 107
rigid atoms, others: [37, 38, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 256
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042726 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1C1=NOC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 66, 107, 107, 107, 107, 66, 66, 66, 66, 31, 7, 1, 1, 1, 1, 66, 66, 66, 107, 107] 107
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 168
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042726 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042726
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042726/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042726
Building REAL300000042727
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042727'
/scratch/stefan/7769623/working/building/REAL300000042727 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042727

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042727/0 /scratch/stefan/7769623/working/building/REAL300000042727 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/799
`/scratch/stefan/7769623/working/3D/799' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC=C2OC(F)(F)F)=C1)

`REAL300000042727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042727 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC=C2OC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 99, 99, 99, 21, 99, 99, 99, 168, 168, 168, 168, 1, 1, 1, 1, 5, 21, 198, 99, 32, 99, 1] 336
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 23, 24, 25, 26] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 582
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042727 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC=C2OC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 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: [99, 99, 99, 99, 99, 99, 99, 62, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 22, 23, 99, 99, 99, 99, 62, 12, 2, 1, 1, 1, 99] 336
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 274
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042727 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042727
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042727/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042727
Building REAL300000042728
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042728'
/scratch/stefan/7769623/working/building/REAL300000042728 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042728

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042728/0 /scratch/stefan/7769623/working/building/REAL300000042728 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/800
`/scratch/stefan/7769623/working/3D/800' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(F)(F)F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042728 none CN1N=CC(C(F)(F)F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 2, 2, 2, 1, 1, 11, 11, 46, 68, 69, 69, 69, 69, 69, 69, 68, 2, 2, 2, 1, 11, 46, 69, 69, 69, 68] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 25] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 166
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042728 none CN1N=CC(C(F)(F)F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 68, 68, 68, 69, 69, 69, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 69, 69, 69, 68, 44, 12, 1, 1, 1, 1] 69
rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27])
total number of confs: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042728 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042728
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042728/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042728
Building REAL300000042729
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042729'
/scratch/stefan/7769623/working/building/REAL300000042729 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042729

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042729/0 /scratch/stefan/7769623/working/building/REAL300000042729 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/801
`/scratch/stefan/7769623/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=C(Br)N2)=C1)

`REAL300000042729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042729 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=C(Br)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 17, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 13, 37, 45, 45, 1] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042729 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=C(Br)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 17, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 44, 45, 45, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 45, 44, 45, 45, 30, 6, 1, 1, 45] 45
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 26])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042729 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042729
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042729/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042729
Building REAL300000042730
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042730'
/scratch/stefan/7769623/working/building/REAL300000042730 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042730

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042730/0 /scratch/stefan/7769623/working/building/REAL300000042730 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/802
`/scratch/stefan/7769623/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C=C1Br)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042730 none COC1=CC2=C(C=C1Br)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 29, 29, 28, 4, 4, 4, 1, 1, 1, 7, 28, 28, 28, 28] 29
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 32, 34, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31])
total number of confs: 54
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042730 none COC1=CC2=C(C=C1Br)NC(=O)C2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 28, 28, 28, 10, 1, 1, 1, 1] 29
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042730 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042730
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042730/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042730
Building REAL300000042731
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042731'
/scratch/stefan/7769623/working/building/REAL300000042731 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042731

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042731/0 /scratch/stefan/7769623/working/building/REAL300000042731 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/803
`/scratch/stefan/7769623/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(N2C(C)=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2C)C=C1OC)

`REAL300000042731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042731 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2C)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 82, 149, 149, 149, 149, 149, 149, 149, 149, 7, 7, 1, 1, 1, 3, 4, 4, 4, 1, 1, 7, 7, 7, 7, 35, 82, 149, 149, 149, 149, 7, 7, 7, 1, 4, 4, 4] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 47, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042731 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2C)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 149, 149, 149, 47, 47, 47, 47, 47, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 149, 149, 149, 201, 201, 201, 201, 149, 149, 47, 47, 47, 47, 20, 4, 1, 1, 1, 1, 47, 47, 47, 149, 201, 201, 201] 201
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 422
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042731 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=C2C)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 7, 7, 7, 16, 17, 17, 17, 7, 7, 2, 2, 2, 1, 8, 26, 47, 47, 47, 47, 2, 2, 2, 7, 16, 16, 16] 201
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 24, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042731 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042731
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042731/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042731
Building REAL300000042732
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042732'
/scratch/stefan/7769623/working/building/REAL300000042732 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042732

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042732/0 /scratch/stefan/7769623/working/building/REAL300000042732 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/804
`/scratch/stefan/7769623/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2OCCCC2=C1)

`REAL300000042732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042732 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2OCCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 91, 91, 91, 91, 91, 91, 91, 91, 91, 44, 44, 44, 10, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 91] 91
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 148
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042732 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C2OCCCC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 57, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 57, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 1, 1, 1] 91
rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 194
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042732 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042732
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042732/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042732
Building REAL300000042733
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042733'
/scratch/stefan/7769623/working/building/REAL300000042733 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042733

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042733/0 /scratch/stefan/7769623/working/building/REAL300000042733 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/805
`/scratch/stefan/7769623/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)NC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)CC1)

`REAL300000042733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042733 none CCOC(=O)NC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 12, 7, 12, 1, 1, 1, 1, 1, 1, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 74, 74, 74, 74, 74, 7, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 39, 40, 42, 21, 22, 41, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042733 none CCOC(=O)NC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)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', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 174, 164, 122, 164, 45, 45, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 201, 201, 201, 201, 201, 122, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 45, 45, 45, 45] 201
rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 679
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042733 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042733
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042733/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042733
Building REAL300000042734
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042734'
/scratch/stefan/7769623/working/building/REAL300000042734 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042734

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042734/0 /scratch/stefan/7769623/working/building/REAL300000042734 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/806
`/scratch/stefan/7769623/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN(C(=O)OC(C)(C)C)C1)

`REAL300000042734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042734 none COC(=O)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 4, 1, 4, 1, 1, 1, 1, 8, 8, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 17, 20, 21, 20, 1, 4, 4, 4, 1, 1, 1, 1, 42, 42, 42, 42, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 191
rigid atoms, others: [32, 33, 2, 50, 4, 5, 6, 7, 40, 39, 34, 18, 19, 20, 27, 51, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042734 none COC(=O)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [91, 91, 42, 91, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 42, 42, 82, 82, 101, 102, 102, 102, 42, 91, 91, 91, 42, 42, 42, 42, 1, 1, 1, 1, 42, 42, 102, 102, 102, 102, 102, 102, 102, 102, 102, 42, 42] 191
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 415
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042734 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042734
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042734/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042734
Building REAL300000042735
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042735'
/scratch/stefan/7769623/working/building/REAL300000042735 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042735

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042735/0 /scratch/stefan/7769623/working/building/REAL300000042735 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/807
`/scratch/stefan/7769623/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C(Cl)=C1)

`REAL300000042735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042735 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 101, 101, 100, 101, 101, 101, 101, 52, 52, 52, 10, 1, 1, 1, 1, 101, 101, 101] 101
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 171
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042735 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 56, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 101, 101, 101, 101, 1, 1, 1] 101
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 207
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042735 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042735
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042735/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042735
Building REAL300000042736
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042736'
/scratch/stefan/7769623/working/building/REAL300000042736 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042736

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042736/0 /scratch/stefan/7769623/working/building/REAL300000042736 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/808
`/scratch/stefan/7769623/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=CC=N2)=C1)

`REAL300000042736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042736 none O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 59, 59, 59, 59, 59, 108, 148, 148, 148, 148, 148, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 108, 108, 148, 148, 148, 148, 1] 148
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 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: REAL300000042736 none O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 148, 148, 148, 148, 95, 95, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 148] 148
rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 242
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042736 none O=C([O-])C1=CC=CC(N=NC2CCCC2CC2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [59, 59, 59, 59, 59, 58, 58, 13, 13, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 59] 148
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042736 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042736
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042736/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042736
Building REAL300000042737
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042737'
/scratch/stefan/7769623/working/building/REAL300000042737 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042737

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042737/0 /scratch/stefan/7769623/working/building/REAL300000042737 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/809
`/scratch/stefan/7769623/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC(C)(C)CC(C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042737 none COC(=O)CC(C)(C)CC(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 16, 21, 13, 11, 13, 13, 8, 4, 8, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 16, 16, 13, 13, 13, 13, 13, 13, 11, 11, 8, 8, 8, 8, 1, 1, 1, 1] 21
rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 95
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042737 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042737
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042737/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042737
Building REAL300000042738
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042738'
/scratch/stefan/7769623/working/building/REAL300000042738 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042738

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042738/0 /scratch/stefan/7769623/working/building/REAL300000042738 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/810
`/scratch/stefan/7769623/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C(F)(F)F)N=C3CCCCN32)=C1)

`REAL300000042738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042738 none O=C([O-])C1=CC=CC(NN=CC2=C(C(F)(F)F)N=C3CCCCN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 38, 38, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 10, 38, 57, 57, 57, 57, 57, 57, 57, 57, 1] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 89
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042738 none O=C([O-])C1=CC=CC(NN=CC2=C(C(F)(F)F)N=C3CCCCN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 57, 57, 39, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 39, 9, 1, 1, 1, 1, 1, 1, 1, 1, 57] 57
rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 38, 24, 25, 26, 27, 28, 29])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042738 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042738
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042738/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042738
Building REAL300000042739
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042739'
/scratch/stefan/7769623/working/building/REAL300000042739 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042739

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042739/0 /scratch/stefan/7769623/working/building/REAL300000042739 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/811
`/scratch/stefan/7769623/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1Br)

`REAL300000042739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042739 none CC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 19, 19, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 18, 18, 18, 18, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 17, 18, 19, 20, 21, 22, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042739 none CC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 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: [18, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 18, 18, 18, 18, 18, 19, 19, 19, 18, 18, 10, 1, 1, 1, 1, 18] 19
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042739 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042739
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042739/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042739
Building REAL300000042740
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042740'
/scratch/stefan/7769623/working/building/REAL300000042740 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042740

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042740/0 /scratch/stefan/7769623/working/building/REAL300000042740 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/812
`/scratch/stefan/7769623/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)=C1)

`REAL300000042740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042740 none O=C([O-])C1=CC=CC(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 51, 96, 101, 101, 96, 96, 101, 101, 51, 86, 86, 86, 1, 1, 1, 1, 51, 96, 96, 101, 101, 101, 101, 86, 86, 86, 86, 86, 86, 86, 1] 119
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 518
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: REAL300000042740 none O=C([O-])C1=CC=CC(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 86, 86, 86, 86, 86, 86, 35, 35, 8, 1, 8, 20, 26, 26, 20, 20, 26, 26, 1, 1, 1, 1, 86, 86, 86, 86, 8, 20, 20, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 86] 119
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 10, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41])
total number of confs: 212
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042740 none O=C([O-])C1=CC=CC(N=NC(CC2=CC=C(Br)C=C2)C2CCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 101, 101, 101, 101, 101, 101, 47, 47, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 101, 101, 101, 101, 9, 3, 3, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 101] 119
rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 214
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042740 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042740
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042740/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042740
Building REAL300000042741
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042741'
/scratch/stefan/7769623/working/building/REAL300000042741 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042741

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042741/0 /scratch/stefan/7769623/working/building/REAL300000042741 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/813
`/scratch/stefan/7769623/working/3D/813' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C(C)(C)C)

`REAL300000042741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042741 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 10, 10, 51, 82, 82, 82, 82, 82, 83, 83, 82, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 10, 51, 82, 82, 82, 82, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 83
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 183
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042741 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 82, 76, 82, 82, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 82, 82, 83, 83, 83, 83, 83, 83, 82, 82, 44, 12, 1, 1, 1, 1, 82, 83, 83, 83, 83, 83, 83, 83, 83, 83] 83
rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042741 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042741
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042741/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042741
Building REAL300000042742
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042742'
/scratch/stefan/7769623/working/building/REAL300000042742 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042742

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042742/0 /scratch/stefan/7769623/working/building/REAL300000042742 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/814
`/scratch/stefan/7769623/working/3D/814' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(CC3CCC3)=C2)=C1)

`REAL300000042742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042742 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(CC3CCC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 93, 93, 67, 93, 93, 141, 201, 201, 201, 93, 1, 1, 1, 1, 9, 33, 93, 93, 93, 141, 141, 201, 201, 201, 201, 201, 201, 201, 93, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 768
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042742 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(CC3CCC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 150, 72, 72, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 150, 72, 17, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 201] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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, 32, 40, 41])
total number of confs: 481
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042742 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(CC3CCC3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 1, 93, 93, 93, 93, 52, 10, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 17, 17, 1, 93] 201
rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042742 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042742
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042742/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042742
Building REAL300000042743
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042743'
/scratch/stefan/7769623/working/building/REAL300000042743 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042743

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042743/0 /scratch/stefan/7769623/working/building/REAL300000042743 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/815
`/scratch/stefan/7769623/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1)

`REAL300000042743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042743 none CCOC(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [54, 27, 13, 1, 13, 1, 1, 1, 1, 1, 1, 4, 4, 20, 59, 59, 59, 59, 59, 60, 60, 59, 1, 54, 54, 54, 54, 54, 1, 1, 1, 4, 20, 59, 59, 59, 59] 159
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042743 none CCOC(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [159, 152, 150, 59, 150, 59, 59, 59, 59, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 59, 159, 159, 159, 159, 159, 59, 59, 59, 40, 10, 1, 1, 1, 1] 159
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 396
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042743 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042743
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042743/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042743
Building REAL300000042744
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042744'
/scratch/stefan/7769623/working/building/REAL300000042744 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042744

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042744/0 /scratch/stefan/7769623/working/building/REAL300000042744 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/816
`/scratch/stefan/7769623/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(F)=C(Cl)C=C23)=C1)

`REAL300000042744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042744 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(F)=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 49, 49, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 13, 49, 86, 86, 86, 86, 1] 86
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 138
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042744 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(F)=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 86, 86, 86, 86, 58, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 57, 10, 1, 1, 1, 1, 86] 86
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 24, 25, 26, 27])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042744 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042744
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042744/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042744
Building REAL300000042745
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042745'
/scratch/stefan/7769623/working/building/REAL300000042745 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042745

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042745/0 /scratch/stefan/7769623/working/building/REAL300000042745 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/817
`/scratch/stefan/7769623/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(I)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042745 none CN1N=CC(I)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 34, 45, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 1, 12, 34, 45, 45, 45, 45] 45
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 101
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042745 none CN1N=CC(I)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'I', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 18, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 38, 12, 1, 1, 1, 1] 45
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042745 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042745
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042745/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042745
Building REAL300000042746
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042746'
/scratch/stefan/7769623/working/building/REAL300000042746 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042746

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042746/0 /scratch/stefan/7769623/working/building/REAL300000042746 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/818
`/scratch/stefan/7769623/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(OC(F)(F)F)C=C32)=CC=C1)

`REAL300000042746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042746 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(OC(F)(F)F)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 46, 46, 46, 46, 46, 46, 46, 46, 46, 138, 138, 138, 138, 46, 46, 1, 1, 1, 1, 12, 46, 46, 46, 46, 1, 1, 1] 139
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 207
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042746 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(OC(F)(F)F)C=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [47, 46, 47, 46, 46, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 1, 1, 46, 46, 46, 46, 7, 1, 1, 1, 1, 46, 46, 46] 139
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 34, 33, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042746 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042746
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042746/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042746
Building REAL300000042747
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042747'
/scratch/stefan/7769623/working/building/REAL300000042747 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042747

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042747/0 /scratch/stefan/7769623/working/building/REAL300000042747 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/819
`/scratch/stefan/7769623/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(F)C(Br)=C32)=CC=C1)

`REAL300000042747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042747 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(F)C(Br)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 10, 18, 18, 18, 1, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042747 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(F)C(Br)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 18, 19, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 7, 1, 1, 1, 18, 18, 18] 19
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042747 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042747
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042747/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042747
Building REAL300000042748
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042748'
/scratch/stefan/7769623/working/building/REAL300000042748 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042748

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042748/0 /scratch/stefan/7769623/working/building/REAL300000042748 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/820
`/scratch/stefan/7769623/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Cl)C=C1O)

`REAL300000042748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042748 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [3, 1, 1, 1, 1, 1, 10, 10, 40, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 4, 4, 4, 1, 10, 40, 91, 91, 91, 91, 1, 2] 182
rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042748 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Cl)C=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [91, 91, 91, 91, 57, 57, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 91, 91, 91, 91, 91, 91, 91, 91, 91, 57, 13, 1, 1, 1, 1, 91, 182] 182
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042748 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042748
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042748/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042748
Building REAL300000042749
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042749'
/scratch/stefan/7769623/working/building/REAL300000042749 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042749

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042749/0 /scratch/stefan/7769623/working/building/REAL300000042749 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/821
`/scratch/stefan/7769623/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=C(Cl)N=CC=C3S2)=C1)

`REAL300000042749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042749 none O=C([O-])C1=CC=CC(NN=CC2=CC3=C(Cl)N=CC=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 42, 42, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 13, 42, 66, 66, 66, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042749 none O=C([O-])C1=CC=CC(NN=CC2=CC3=C(Cl)N=CC=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 48, 9, 1, 1, 1, 66] 66
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042749 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042749
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042749/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042749
Building REAL300000042750
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042750'
/scratch/stefan/7769623/working/building/REAL300000042750 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042750

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042750/0 /scratch/stefan/7769623/working/building/REAL300000042750 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/822
`/scratch/stefan/7769623/working/3D/822' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=CC=NC(Cl)=C3S2)=C1)

`REAL300000042750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042750 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC=NC(Cl)=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 36, 36, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 11, 36, 51, 51, 51, 1] 51
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042750 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC=NC(Cl)=C3S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 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, 51, 51, 51, 51, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 40, 8, 1, 1, 1, 51] 51
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 112
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042750 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042750
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042750/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042750
Building REAL300000042751
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042751'
/scratch/stefan/7769623/working/building/REAL300000042751 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042751

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042751/0 /scratch/stefan/7769623/working/building/REAL300000042751 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/823
`/scratch/stefan/7769623/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2(C3CCCCO3)CCC2)=C1)

`REAL300000042751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042751 none O=C([O-])C1=CC=CC(N=NCC2(C3CCCCO3)CCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 9, 9, 40, 95, 113, 113, 113, 113, 113, 95, 95, 95, 1, 1, 1, 1, 39, 40, 113, 113, 113, 113, 113, 113, 113, 113, 113, 95, 95, 95, 95, 95, 95, 1] 113
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 345
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: REAL300000042751 none O=C([O-])C1=CC=CC(N=NCC2(C3CCCCO3)CCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 113, 113, 113, 79, 79, 23, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 113, 113, 113, 113, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 113] 113
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 216
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042751 none O=C([O-])C1=CC=CC(N=NCC2(C3CCCCO3)CCC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [95, 95, 95, 95, 95, 95, 95, 48, 48, 10, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 95, 95, 95, 95, 10, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 95] 113
rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42])
total number of confs: 168
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042751 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042751
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042751/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042751
Building REAL300000042752
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042752'
/scratch/stefan/7769623/working/building/REAL300000042752 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042752

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042752/0 /scratch/stefan/7769623/working/building/REAL300000042752 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/824
`/scratch/stefan/7769623/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C(=O)C(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(C)=CC=C21)

`REAL300000042752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042752 none CCCN1C(=O)C(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(C)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 5, 38, 38, 38, 38, 38, 39, 39, 38, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 7, 5, 38, 38, 38, 38, 1, 2, 2, 2, 1, 1] 73
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 41, 42, 18, 19, 20, 21, 22, 23, 24, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042752 none CCCN1C(=O)C(=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC(C)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 38, 38, 38, 38, 38, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 38, 26, 38, 38, 38, 73, 73, 73, 73, 73, 73, 73, 12, 1, 1, 1, 1, 38, 39, 39, 39, 38, 38] 73
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 351
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042752 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042752
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042752/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042752
Building REAL300000042753
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042753'
/scratch/stefan/7769623/working/building/REAL300000042753 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042753

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042753/0 /scratch/stefan/7769623/working/building/REAL300000042753 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/825
`/scratch/stefan/7769623/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(OC(F)(F)F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042753 none COC1=CC=CC(OC(F)(F)F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 1, 1, 12, 12, 53, 105, 105, 105, 105, 105, 106, 106, 105, 4, 4, 4, 1, 1, 1, 12, 53, 105, 105, 105, 105] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 12, 13, 28, 29, 30] set([0, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36])
total number of confs: 277
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042753 none COC1=CC=CC(OC(F)(F)F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 105, 105, 105, 105, 105, 105, 105, 194, 200, 200, 200, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 136, 136, 136, 105, 105, 105, 25, 6, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 371
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042753 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042753
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042753/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042753
Building REAL300000042754
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042754'
/scratch/stefan/7769623/working/building/REAL300000042754 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042754

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042754/0 /scratch/stefan/7769623/working/building/REAL300000042754 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/826
`/scratch/stefan/7769623/working/3D/826' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC=C1Br)

`REAL300000042754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042754 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 25, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 2, 2, 2, 1, 7, 25, 36, 36, 36, 36, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 23, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28, 29])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042754 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=NC=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 35, 35, 36, 36, 36, 36, 28, 12, 1, 1, 1, 1, 36] 36
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042754 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042754
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042754/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042754
Building REAL300000042755
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042755'
/scratch/stefan/7769623/working/building/REAL300000042755 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042755

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042755/0 /scratch/stefan/7769623/working/building/REAL300000042755 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/827
`/scratch/stefan/7769623/working/3D/827' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Br)C=C1F)

`REAL300000042755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042755 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 10, 10, 38, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 38, 47, 47, 47, 47, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 24, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042755 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Br)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 47, 33, 39, 47, 47, 47, 47, 33, 11, 1, 1, 1, 1, 47] 47
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042755 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042755
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042755/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042755
Building REAL300000042756
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042756'
/scratch/stefan/7769623/working/building/REAL300000042756 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042756

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042756/0 /scratch/stefan/7769623/working/building/REAL300000042756 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/828
`/scratch/stefan/7769623/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC2CCC(N=NC3=CC=CC(C(=O)[O-])=C3)C21)

`REAL300000042756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042756 none CC(C)(C)OC(=O)N1CCC2CCC(N=NC3=CC=CC(C(=O)[O-])=C3)C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [14, 11, 14, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 1] 40
rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 44, 40, 43, 41, 25, 49, 42, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042756 none CC(C)(C)OC(=O)N1CCC2CCC(N=NC3=CC=CC(C(=O)[O-])=C3)C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 40, 40, 40, 39, 24, 39, 24, 24, 24, 24, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 24] 40
rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49])
total number of confs: 108
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042756 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042756
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042756/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042756
Building REAL300000042757
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042757'
/scratch/stefan/7769623/working/building/REAL300000042757 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042757

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042757/0 /scratch/stefan/7769623/working/building/REAL300000042757 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/829
`/scratch/stefan/7769623/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042757 none CC(C)(C)OC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 32, 31, 10, 1, 10, 1, 1, 1, 1, 1, 9, 9, 41, 71, 71, 71, 71, 71, 71, 71, 71, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 9, 41, 71, 71, 71, 71] 201
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 23] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042757 none CC(C)(C)OC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 145, 71, 145, 71, 71, 71, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71, 40, 8, 1, 1, 1, 1] 201
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 449
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042757 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042757
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042757/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042757
Building REAL300000042758
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042758'
/scratch/stefan/7769623/working/building/REAL300000042758 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042758

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042758/0 /scratch/stefan/7769623/working/building/REAL300000042758 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/830
`/scratch/stefan/7769623/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CN(C(=O)OC(C)(C)C)CC1N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042758 none CC1CN(C(=O)OC(C)(C)C)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 23, 29, 29, 29, 1, 1, 1, 13, 13, 56, 56, 56, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 56, 56, 56, 56] 154
rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 41, 11, 12, 13, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45])
total number of confs: 161
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042758 none CC1CN(C(=O)OC(C)(C)C)CC1N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 98, 98, 149, 154, 154, 154, 56, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 154, 154, 154, 154, 154, 154, 154, 154, 154, 56, 56, 56, 1, 1, 1, 1] 154
rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 374
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042758 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042758
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042758/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042758
Building REAL300000042759
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042759'
/scratch/stefan/7769623/working/building/REAL300000042759 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042759

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042759/0 /scratch/stefan/7769623/working/building/REAL300000042759 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/831
`/scratch/stefan/7769623/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC=C2Br)=C1)

`REAL300000042759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042759 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
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, 1, 1, 1, 1, 10, 41, 41, 74, 74, 74, 64, 74, 74, 74, 1, 1, 1, 1, 10, 41, 148, 74, 74, 74, 1] 148
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28])
total number of confs: 299
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042759 none O=C([O-])C1=CC=CC(NN=CC2=C(O)C=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 53, 10, 2, 1, 1, 1, 74] 148
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 164
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042759 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042759
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042759/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042759
Building REAL300000042760
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042760'
/scratch/stefan/7769623/working/building/REAL300000042760 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042760

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042760/0 /scratch/stefan/7769623/working/building/REAL300000042760 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/832
`/scratch/stefan/7769623/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(SC(F)(F)F)=C1)

`REAL300000042760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042760 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(SC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 86, 86, 86, 86, 86, 201, 201, 201, 201, 86, 19, 19, 19, 4, 1, 1, 1, 1, 86, 86, 86, 86] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 295
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042760 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(SC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 1, 11, 11, 11, 46, 86, 86, 86, 86, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 245
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042760 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042760
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042760/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042760
Building REAL300000042761
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042761'
/scratch/stefan/7769623/working/building/REAL300000042761 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042761

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042761/0 /scratch/stefan/7769623/working/building/REAL300000042761 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/833
`/scratch/stefan/7769623/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1Br)

`REAL300000042761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042761 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 7, 7, 34, 70, 70, 69, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 3, 3, 3, 1, 7, 34, 70, 70, 69, 70, 1] 70
rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 139
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042761 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 70, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 47, 13, 1, 1, 1, 1, 70] 70
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 110
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042761 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042761
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042761/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042761
Building REAL300000042762
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042762'
/scratch/stefan/7769623/working/building/REAL300000042762 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042762

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042762/0 /scratch/stefan/7769623/working/building/REAL300000042762 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/834
`/scratch/stefan/7769623/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2Cl)=C1)

`REAL300000042762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042762 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 11, 35, 35, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 11, 35, 38, 38, 38, 1] 38
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042762 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(Br)=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 28, 8, 1, 1, 1, 38] 38
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042762 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042762
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042762/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042762
Building REAL300000042763
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042763'
/scratch/stefan/7769623/working/building/REAL300000042763 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042763

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042763/0 /scratch/stefan/7769623/working/building/REAL300000042763 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/835
`/scratch/stefan/7769623/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1)

`REAL300000042763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042763 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [28, 25, 28, 28, 14, 9, 14, 1, 1, 1, 1, 1, 1, 7, 7, 23, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 7, 23, 44, 44, 44, 44] 116
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042763 none CC(C)(C)OC(=O)NC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 116, 116, 116, 90, 74, 90, 44, 44, 44, 44, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 116, 116, 116, 116, 116, 116, 116, 116, 116, 74, 44, 44, 29, 8, 1, 1, 1, 1] 116
rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 279
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042763 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042763
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042763/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042763
Building REAL300000042764
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042764'
/scratch/stefan/7769623/working/building/REAL300000042764 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042764

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042764/0 /scratch/stefan/7769623/working/building/REAL300000042764 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/836
`/scratch/stefan/7769623/working/3D/836' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(CNC(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL300000042764 none CCOCC(CNC(=O)OC(C)(C)C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 65, 35, 20, 5, 20, 33, 105, 160, 160, 174, 174, 174, 174, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 66, 66, 35, 35, 20, 33, 33, 105, 174, 174, 174, 174, 174, 174, 174, 174, 174, 1, 1, 1, 1] 201
rigid atoms, others: [48, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 712
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042764 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042764
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042764/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042764
Building REAL300000042765
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042765'
/scratch/stefan/7769623/working/building/REAL300000042765 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042765

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042765/0 /scratch/stefan/7769623/working/building/REAL300000042765 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/837
`/scratch/stefan/7769623/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042765 none CCC(C)C1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 12, 68, 184, 184, 184, 184, 184, 184, 184, 184, 1, 1, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 13, 13, 13, 68, 184, 184, 184, 184, 1, 1] 187
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 42, 43, 21, 22] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 360
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042765 none CCC(C)C1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [187, 187, 184, 187, 116, 184, 184, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 184, 184, 187, 187, 187, 187, 187, 187, 187, 187, 187, 184, 184, 51, 51, 51, 12, 1, 1, 1, 1, 184, 184] 187
rigid atoms, others: [38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 556
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042765 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042765
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042765/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042765
Building REAL300000042766
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042766'
/scratch/stefan/7769623/working/building/REAL300000042766 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042766

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042766/0 /scratch/stefan/7769623/working/building/REAL300000042766 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/838
`/scratch/stefan/7769623/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)SC(C)=C1)

`REAL300000042766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042766 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)SC(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 121, 47, 47, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 172, 172, 172, 172, 172, 172, 141, 141, 141, 141, 141, 121, 121, 8, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 14, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 682
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042766 none CCCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)SC(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 9, 1, 9, 9, 60, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 36, 36, 60, 172, 172, 172, 172, 2, 2, 2, 2, 2, 2, 1] 201
rigid atoms, others: [3, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 472
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042766 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042766
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042766/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042766
Building REAL300000042767
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042767'
/scratch/stefan/7769623/working/building/REAL300000042767 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042767

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042767/0 /scratch/stefan/7769623/working/building/REAL300000042767 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/839
`/scratch/stefan/7769623/working/3D/839' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)C=N1)

`REAL300000042767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042767 none CN1C=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 5, 19, 19, 69, 98, 98, 98, 98, 98, 98, 98, 98, 4, 4, 1, 1, 2, 2, 2, 1, 19, 68, 98, 98, 98, 98, 4, 1] 98
rigid atoms, others: [0, 1, 2, 3, 4, 34, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042767 none CN1C=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 77, 77, 77, 56, 56, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 77, 98, 98, 98, 98, 98, 98, 56, 12, 1, 1, 1, 1, 77, 98] 98
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 162
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042767 none CN1C=C(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 4, 4, 1, 1, 1, 1, 1, 7, 7, 37, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 4, 4, 5, 5, 5, 5, 7, 37, 77, 77, 77, 77, 1, 5] 98
rigid atoms, others: [33, 3, 4, 5, 6, 7, 19, 20] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042767 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042767
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042767/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042767
Building REAL300000042768
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042768'
/scratch/stefan/7769623/working/building/REAL300000042768 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042768

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042768/0 /scratch/stefan/7769623/working/building/REAL300000042768 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/840
`/scratch/stefan/7769623/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1Cl)

`REAL300000042768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042768 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 10, 10, 50, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 3, 3, 3, 1, 10, 50, 121, 121, 121, 121, 1, 1] 126
rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 30])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042768 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 121, 121, 121, 62, 62, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 121, 121, 120, 120, 126, 126, 126, 121, 62, 12, 1, 1, 1, 1, 121, 121] 126
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 201
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042768 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042768
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042768/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042768
Building REAL300000042769
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042769'
/scratch/stefan/7769623/working/building/REAL300000042769 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042769

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042769/0 /scratch/stefan/7769623/working/building/REAL300000042769 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/841
`/scratch/stefan/7769623/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1OCCCC2=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042769 none COC1=CC=CC2=C1OCCCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 36, 36, 35, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35] 36
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042769 none COC1=CC=CC2=C1OCCCC2=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 1, 1, 1, 1] 36
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 60
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042769 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042769
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042769/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042769
Building REAL300000042770
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042770'
/scratch/stefan/7769623/working/building/REAL300000042770 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042770

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042770/0 /scratch/stefan/7769623/working/building/REAL300000042770 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/842
`/scratch/stefan/7769623/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)=C1)

`REAL300000042770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042770 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 11, 35, 42, 42, 42, 42, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042770 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 42, 42, 42, 42, 27, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 42, 42, 42, 42, 27, 9, 4, 1, 1, 1, 1, 42] 42
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 85
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042770 none O=C([O-])C1=CC=CC(NN=CC2=CN(C3=CC=C(F)C=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 42, 42, 42, 42, 26, 6, 6, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 42, 42, 42, 42, 26, 6, 1, 4, 4, 4, 4, 42] 42
rigid atoms, others: [10, 11, 12, 13, 14, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042770 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042770/1 /scratch/stefan/7769623/working/building/REAL300000042770 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/843
`/scratch/stefan/7769623/working/3D/843' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)=C1)

`REAL300000042770.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042770/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042770 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 1, 1, 1, 1, 60, 61, 166, 166, 166, 166, 166, 1] 166
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 23, 24, 25, 26] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042770 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [166, 166, 166, 166, 166, 166, 166, 111, 111, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 166, 166, 166, 166, 25, 25, 3, 1, 1, 1, 1, 166] 166
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 289
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042770 none O=C([O-])C1=CC=CC(N=NCC2=CN(C3=CC=C(F)C=C3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [166, 166, 166, 166, 166, 166, 166, 67, 67, 9, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 166, 166, 166, 166, 9, 9, 1, 3, 3, 3, 3, 166] 166
rigid atoms, others: [10, 11, 12, 13, 14, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 244
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042770 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042770
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042770/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042770/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042770
Building REAL300000042771
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042771'
/scratch/stefan/7769623/working/building/REAL300000042771 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042771

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042771/0 /scratch/stefan/7769623/working/building/REAL300000042771 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/844
`/scratch/stefan/7769623/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2CC(F)(F)F)=C1)

`REAL300000042771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042771 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2CC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 58, 58, 151, 151, 101, 151, 151, 151, 169, 169, 169, 169, 1, 1, 1, 1, 13, 58, 151, 151, 147, 151, 169, 169, 1] 169
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 514
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042771 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2CC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 151, 151, 151, 151, 151, 71, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 151, 151, 151, 151, 71, 11, 1, 1, 1, 1, 6, 6, 151] 169
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 303
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042771 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042771
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042771/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042771
Building REAL300000042772
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042772'
/scratch/stefan/7769623/working/building/REAL300000042772 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042772

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042772/0 /scratch/stefan/7769623/working/building/REAL300000042772 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/845
`/scratch/stefan/7769623/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=N1)

`REAL300000042772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042772 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 11, 11, 36, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 2, 2, 2, 1, 11, 36, 47, 47, 47, 47] 47
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042772 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Br)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 47, 47, 47, 47, 47, 34, 10, 1, 1, 1, 1] 47
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042772 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042772
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042772/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042772
Building REAL300000042773
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042773'
/scratch/stefan/7769623/working/building/REAL300000042773 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042773

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042773/0 /scratch/stefan/7769623/working/building/REAL300000042773 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/846
`/scratch/stefan/7769623/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1)

`REAL300000042773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042773 none O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 143, 171, 176, 176, 173, 176, 176, 29, 90, 90, 90, 90, 90, 1, 1, 1, 1, 9, 143, 143, 171, 171, 176, 176, 176, 176, 176, 90, 90, 90, 90, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 726
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042773 none O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 38, 10, 10, 1, 10, 62, 75, 83, 83, 75, 83, 83, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 38, 62, 62, 75, 75, 83, 83, 83, 83, 83, 1, 1, 1, 1, 90] 201
rigid atoms, others: [39, 40, 41, 10, 19, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 479
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042773 none O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [176, 176, 176, 176, 176, 176, 176, 91, 28, 28, 6, 3, 1, 1, 1, 1, 1, 1, 1, 28, 83, 83, 83, 83, 83, 176, 176, 176, 176, 91, 6, 6, 3, 3, 1, 1, 1, 1, 1, 83, 83, 83, 83, 176] 201
rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43])
total number of confs: 436
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042773 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042773/1 /scratch/stefan/7769623/working/building/REAL300000042773 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/847
`/scratch/stefan/7769623/working/3D/847' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1)

`REAL300000042773.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042773/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042773 none O=C([O-])C1=CC=CC(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 117, 135, 159, 159, 143, 159, 159, 49, 137, 137, 137, 137, 137, 1, 1, 1, 1, 49, 125, 125, 135, 131, 159, 159, 159, 159, 159, 137, 137, 137, 137, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 793
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042773 none O=C([O-])C1=CC=CC(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 59, 59, 11, 1, 11, 35, 47, 67, 67, 52, 67, 67, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 11, 39, 39, 47, 47, 67, 67, 67, 67, 67, 1, 1, 1, 1, 137] 201
rigid atoms, others: [39, 40, 41, 10, 19, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 490
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042773 none O=C([O-])C1=CC=CC(N=NC(CCC2=CC=CC=C2)C2=CC=CC=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 159, 159, 159, 159, 77, 77, 19, 5, 3, 1, 1, 1, 1, 1, 1, 1, 19, 67, 67, 67, 67, 67, 159, 159, 159, 159, 19, 5, 5, 3, 3, 1, 1, 1, 1, 1, 67, 67, 67, 67, 159] 201
rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43])
total number of confs: 337
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042773 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042773
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042773/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042773/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042773
Building REAL300000042774
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042774'
/scratch/stefan/7769623/working/building/REAL300000042774 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042774

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042774/0 /scratch/stefan/7769623/working/building/REAL300000042774 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/848
`/scratch/stefan/7769623/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1)

`REAL300000042774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042774 none CC(C)(C)OC(=O)NC1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [35, 30, 35, 35, 13, 8, 13, 1, 1, 1, 1, 1, 1, 4, 4, 27, 52, 52, 52, 52, 52, 53, 53, 52, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 1, 4, 27, 52, 52, 52, 52, 1] 168
rigid atoms, others: [43, 36, 7, 8, 9, 10, 11, 12, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42])
total number of confs: 197
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042774 none CC(C)(C)OC(=O)NC1=CN=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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
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, 168, 130, 104, 130, 52, 52, 52, 52, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 52, 168, 168, 168, 168, 168, 168, 168, 168, 168, 104, 52, 27, 8, 1, 1, 1, 1, 52] 168
rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042774 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042774
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042774/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042774
Building REAL300000042775
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042775'
/scratch/stefan/7769623/working/building/REAL300000042775 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042775

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042775/0 /scratch/stefan/7769623/working/building/REAL300000042775 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/849
`/scratch/stefan/7769623/working/3D/849' -> `0.mol2'
Preparing input files

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

`REAL300000042775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042775 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 48, 48, 56, 56, 55, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 13, 48, 56, 56, 56, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 24, 25, 26, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042775 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)F)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 31, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 56, 56, 56, 56, 31, 7, 1, 1, 1, 56] 56
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042775 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042775
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042775/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042775
Building REAL300000042776
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042776'
/scratch/stefan/7769623/working/building/REAL300000042776 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042776

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042776/0 /scratch/stefan/7769623/working/building/REAL300000042776 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/850
`/scratch/stefan/7769623/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC)

`REAL300000042776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042776 none COC1=CC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 3, 4, 4, 4, 1, 10, 48, 117, 117, 117, 117, 1, 4, 4, 4] 148
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 19, 20, 21, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36])
total number of confs: 227
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042776 none COC1=CC(Cl)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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, 117, 117, 117, 117, 117, 64, 64, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 117, 117, 117, 148, 148, 148, 148, 117, 64, 11, 1, 1, 1, 1, 117, 148, 148, 148] 148
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 292
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042776 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042776
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042776/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042776
Building REAL300000042777
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042777'
/scratch/stefan/7769623/working/building/REAL300000042777 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042777

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042777/0 /scratch/stefan/7769623/working/building/REAL300000042777 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/851
`/scratch/stefan/7769623/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCOC3)N=N2)=C1)

`REAL300000042777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042777 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCOC3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 60, 60, 60, 148, 201, 201, 201, 201, 60, 60, 1, 1, 1, 1, 22, 23, 60, 148, 148, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 717
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042777 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCOC3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 177, 177, 58, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 58, 58, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 413
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042777 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCOC3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 34, 34, 6, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 1, 1, 60, 60, 60, 60, 6, 6, 1, 8, 8, 17, 17, 17, 17, 17, 17, 17, 60] 201
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 148
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042777 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042777/1 /scratch/stefan/7769623/working/building/REAL300000042777 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/852
`/scratch/stefan/7769623/working/3D/852' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCOC3)N=N2)=C1)

`REAL300000042777.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042777/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042777 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCOC3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 50, 50, 50, 151, 201, 201, 201, 201, 50, 50, 1, 1, 1, 1, 9, 39, 50, 151, 151, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042777 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCOC3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 150, 51, 51, 30, 30, 30, 7, 1, 1, 1, 1, 1, 1, 30, 30, 201, 201, 201, 201, 150, 51, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 456
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042777 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCOC3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 24, 4, 4, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 1, 1, 50, 50, 50, 50, 23, 4, 1, 8, 8, 30, 30, 30, 30, 30, 30, 30, 50] 201
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 173
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042777 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042777
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042777/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042777/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042777
Building REAL300000042778
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042778'
/scratch/stefan/7769623/working/building/REAL300000042778 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042778

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042778/0 /scratch/stefan/7769623/working/building/REAL300000042778 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/853
`/scratch/stefan/7769623/working/3D/853' -> `0.mol2'
Preparing input files

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

`REAL300000042778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042778 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(CC(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 13, 41, 41, 45, 45, 43, 45, 73, 73, 73, 73, 45, 45, 1, 1, 1, 1, 13, 41, 45, 45, 73, 73, 45, 45, 1] 73
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042778 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(CC(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [45, 45, 45, 45, 45, 45, 45, 27, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 45, 45, 45, 45, 26, 5, 1, 1, 5, 5, 1, 1, 45] 73
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 34])
total number of confs: 105
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042778 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042778
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042778/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042778
Building REAL300000042779
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042779'
/scratch/stefan/7769623/working/building/REAL300000042779 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042779

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042779/0 /scratch/stefan/7769623/working/building/REAL300000042779 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/854
`/scratch/stefan/7769623/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042779 none CC(C)(C)OC(=O)NCC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 74, 64, 32, 64, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 25, 25, 25, 25, 25, 25, 25, 25, 1, 75, 75, 75, 74, 74, 74, 75, 75, 75, 32, 6, 6, 1, 1, 1, 7, 13, 25, 25, 25, 25, 1] 201
rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14, 48, 40, 41, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47])
total number of confs: 294
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042779 none CC(C)(C)OC(=O)NCC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 192, 160, 192, 67, 25, 25, 9, 25, 25, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 67, 67, 9, 25, 25, 9, 3, 1, 1, 1, 1, 25] 201
rigid atoms, others: [44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48])
total number of confs: 642
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042779 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042779
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042779/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042779
Building REAL300000042780
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042780'
/scratch/stefan/7769623/working/building/REAL300000042780 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042780

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042780/0 /scratch/stefan/7769623/working/building/REAL300000042780 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/855
`/scratch/stefan/7769623/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1)

`REAL300000042780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042780 none CCOC(=O)C1=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 17, 11, 1, 11, 1, 1, 1, 1, 1, 10, 10, 55, 101, 101, 101, 101, 101, 101, 101, 100, 1, 1, 1, 38, 38, 38, 38, 38, 2, 2, 2, 10, 55, 101, 101, 101, 100, 2, 2, 2, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 41, 21, 22, 23] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 338
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042780 none CCOC(=O)C1=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 187, 180, 100, 180, 100, 100, 100, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 100, 101, 100, 201, 201, 201, 201, 201, 101, 101, 101, 34, 8, 1, 1, 1, 1, 101, 101, 101, 100] 201
rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 518
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042780 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042780
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042780/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042780
Building REAL300000042781
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042781'
/scratch/stefan/7769623/working/building/REAL300000042781 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042781

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042781/0 /scratch/stefan/7769623/working/building/REAL300000042781 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/856
`/scratch/stefan/7769623/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=C(Cl)C=C21)

`REAL300000042781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042781 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=C(Cl)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 1, 8, 8, 52, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 51, 79, 79, 79, 78, 1, 1, 1] 79
rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 26] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042781 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C2=CC=C(Cl)C=C21 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [78, 78, 78, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 78, 79, 79, 79, 79, 78, 78, 79, 79, 79, 79, 42, 12, 1, 1, 1, 1, 79, 79, 78] 79
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 139
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042781 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042781
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042781/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042781
Building REAL300000042782
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042782'
/scratch/stefan/7769623/working/building/REAL300000042782 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042782

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042782/0 /scratch/stefan/7769623/working/building/REAL300000042782 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/857
`/scratch/stefan/7769623/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1)

`REAL300000042782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042782 none CCOC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 26, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 43, 87, 87, 87, 87, 87, 87, 87, 87, 1, 43, 43, 43, 42, 42, 1, 1, 7, 43, 87, 87, 87, 87, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 35, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 289
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042782 none CCOC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 183, 177, 87, 177, 87, 87, 87, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 201, 201, 201, 201, 201, 87, 87, 46, 10, 1, 1, 1, 1, 87] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 539
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042782 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042782
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042782/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042782
Building REAL300000042783
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042783'
/scratch/stefan/7769623/working/building/REAL300000042783 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042783

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042783/0 /scratch/stefan/7769623/working/building/REAL300000042783 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/858
`/scratch/stefan/7769623/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CNC2=CC=CC=C12)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042783 none CC(CCC1=CNC2=CC=CC=C12)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 39, 39, 39, 39, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41])
total number of confs: 404
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042783 none CC(CCC1=CNC2=CC=CC=C12)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 41, 85, 106, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 86, 86, 105, 106, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 588
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042783 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042783
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042783/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042783
Building REAL300000042784
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042784'
/scratch/stefan/7769623/working/building/REAL300000042784 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042784

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042784/0 /scratch/stefan/7769623/working/building/REAL300000042784 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/859
`/scratch/stefan/7769623/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1)

`REAL300000042784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042784 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 63, 63, 36, 49, 180, 201, 201, 201, 201, 201, 201, 63, 63, 29, 29, 29, 6, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 63, 63] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 402
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: REAL300000042784 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 5, 40, 48, 162, 201, 201, 201, 201, 201, 201, 201, 201, 5, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 40, 46, 45, 162, 199, 201, 201, 201, 17, 17, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 538
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042784 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 31, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 31, 63, 63, 63, 63, 1, 1, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [1, 35, 36, 41, 42, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042784 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042784
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042784/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042784
Building REAL300000042785
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042785'
/scratch/stefan/7769623/working/building/REAL300000042785 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042785

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042785/0 /scratch/stefan/7769623/working/building/REAL300000042785 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/860
`/scratch/stefan/7769623/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CS1)

`REAL300000042785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042785 none CC(C)(C)OC(=O)NC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 6, 6, 17, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 17, 25, 25, 25, 25, 1] 31
rigid atoms, others: [7, 8, 9, 10, 11, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042785 none CC(C)(C)OC(=O)NC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 31, 31, 31, 25, 31, 25, 25, 25, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 25, 19, 10, 1, 1, 1, 1, 25] 31
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042785 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042785
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042785/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042785
Building REAL300000042786
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042786'
/scratch/stefan/7769623/working/building/REAL300000042786 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042786

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042786/0 /scratch/stefan/7769623/working/building/REAL300000042786 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/861
`/scratch/stefan/7769623/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(Cl)N=CC=C2O1)

`REAL300000042786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042786 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 140, 140, 140, 140, 140, 140, 140, 140, 140, 50, 50, 50, 50, 1, 1, 1, 1, 140, 140, 140] 140
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042786 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 92, 92, 140, 140, 140, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 140, 140, 140, 140, 1, 1, 1] 140
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042786 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042786/1 /scratch/stefan/7769623/working/building/REAL300000042786 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/862
`/scratch/stefan/7769623/working/3D/862' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(Cl)N=CC=C2O1)

`REAL300000042786.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042786/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042786 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 43, 43, 43, 44, 43, 43, 43, 43, 43, 32, 32, 32, 10, 1, 1, 1, 1, 43, 43, 44] 44
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 81
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042786 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=C(Cl)N=CC=C2O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [8, 1, 8, 8, 30, 44, 44, 44, 44, 44, 44, 44, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 44, 44, 44, 43, 1, 1, 1] 44
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 105
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042786 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042786
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042786/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042786/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042786
Building REAL300000042787
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042787'
/scratch/stefan/7769623/working/building/REAL300000042787 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042787

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042787/0 /scratch/stefan/7769623/working/building/REAL300000042787 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/863
`/scratch/stefan/7769623/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OC)=C1OC)

`REAL300000042787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042787 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OC)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [81, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 117, 117, 117, 117, 117, 159, 117, 117, 158, 82, 82, 82, 81, 81, 10, 1, 1, 1, 1, 117, 117, 117, 159, 159, 159, 158, 158, 158] 165
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 530
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042787 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(OC)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 9, 1, 9, 9, 44, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 4, 1, 1, 6, 23, 23, 23, 23, 23, 44, 117, 117, 117, 117, 1, 1, 1, 4, 4, 4, 7, 7, 7] 165
rigid atoms, others: [2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 280
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042787 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042787
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042787/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042787
Building REAL300000042788
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042788'
/scratch/stefan/7769623/working/building/REAL300000042788 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042788

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042788/0 /scratch/stefan/7769623/working/building/REAL300000042788 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/864
`/scratch/stefan/7769623/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)=C1)

`REAL300000042788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042788 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 46, 46, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 13, 46, 93, 93, 93, 93, 93, 93, 93, 93, 1] 93
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 150
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042788 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 68, 22, 22, 3, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 93, 93, 93, 93, 68, 22, 4, 4, 1, 1, 1, 1, 1, 4, 93] 93
rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 219
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042788 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 92, 93, 93, 54, 10, 10, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 93, 92, 93, 93, 54, 10, 1, 1, 4, 4, 2, 4, 4, 1, 93] 93
rigid atoms, others: [37, 10, 11, 12, 13, 14, 15, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042788 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042788
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042788/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042788
Building REAL300000042789
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042789'
/scratch/stefan/7769623/working/building/REAL300000042789 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042789

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042789/0 /scratch/stefan/7769623/working/building/REAL300000042789 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/865
`/scratch/stefan/7769623/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C(F)=C2F)=C1)

`REAL300000042789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042789 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C(F)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 11, 31, 36, 36, 1] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042789 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Br)C(F)=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 15, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 36, 36, 36, 25, 9, 1, 1, 36] 36
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042789 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042789
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042789/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042789
Building REAL300000042790
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042790'
/scratch/stefan/7769623/working/building/REAL300000042790 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042790

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042790/0 /scratch/stefan/7769623/working/building/REAL300000042790 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/866
`/scratch/stefan/7769623/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Br)SC=C2)=C1)

`REAL300000042790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042790 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)SC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 41, 41, 41, 41, 41, 1, 1, 1, 1, 11, 35, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042790 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)SC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 14, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 30, 10, 1, 1, 41] 41
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 25])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042790 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042790
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042790/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042790
Building REAL300000042791
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042791'
/scratch/stefan/7769623/working/building/REAL300000042791 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042791

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042791/0 /scratch/stefan/7769623/working/building/REAL300000042791 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/867
`/scratch/stefan/7769623/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1OC)

`REAL300000042791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042791 none CCOC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 8, 8, 30, 80, 80, 79, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 3, 35, 35, 35, 35, 35, 1, 8, 30, 80, 80, 79, 80, 1, 4, 4, 4] 201
rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 36, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042791 none CCOC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 80, 80, 80, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 80, 80, 80, 80, 140, 201, 201, 201, 201, 201, 80, 51, 11, 1, 1, 1, 1, 80, 140, 140, 140] 201
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 480
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042791 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042791
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042791/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042791
Building REAL300000042792
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042792'
/scratch/stefan/7769623/working/building/REAL300000042792 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042792

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042792/0 /scratch/stefan/7769623/working/building/REAL300000042792 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/868
`/scratch/stefan/7769623/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C3=CC=CC=C23)=C1)

`REAL300000042792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042792 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C3=CC=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 1, 1, 1, 1, 1, 13, 45, 45, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 13, 45, 69, 69, 69, 69, 69, 69, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 104
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042792 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(F)C3=CC=CC=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 48, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 48, 12, 1, 1, 1, 1, 1, 1, 69] 69
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 22, 23, 24, 25, 26, 27])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042792 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042792
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042792/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042792
Building REAL300000042793
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042793'
/scratch/stefan/7769623/working/building/REAL300000042793 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042793

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042793/0 /scratch/stefan/7769623/working/building/REAL300000042793 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/869
`/scratch/stefan/7769623/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CN=C2Br)=C1)

`REAL300000042793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042793 none O=C([O-])C1=CC=CC(NN=CC2=CC=CN=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 13, 37, 41, 41, 41, 1] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042793 none O=C([O-])C1=CC=CC(NN=CC2=CC=CN=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 32, 8, 1, 1, 1, 41] 41
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042793 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042793
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042793/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042793
Building REAL300000042794
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042794'
/scratch/stefan/7769623/working/building/REAL300000042794 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042794

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042794/0 /scratch/stefan/7769623/working/building/REAL300000042794 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/870
`/scratch/stefan/7769623/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)=C1)

`REAL300000042794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042794 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 109, 109, 109, 109, 109, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 33, 109, 109, 193, 193, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042794 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 164, 52, 52, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 164, 52, 18, 18, 5, 5, 1, 1, 1, 1, 201] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42])
total number of confs: 490
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042794 none O=C([O-])C1=CC=CC(NN=CC2=CNN=C2CN2C(=O)C3=CC=CC=C3C2=O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 109, 108, 109, 109, 58, 10, 10, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 109, 108, 109, 109, 58, 10, 1, 1, 8, 8, 16, 16, 16, 16, 109] 201
rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 253
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042794 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042794
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042794/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042794
Building REAL300000042795
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042795'
/scratch/stefan/7769623/working/building/REAL300000042795 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042795

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042795/0 /scratch/stefan/7769623/working/building/REAL300000042795 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/871
`/scratch/stefan/7769623/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OC(F)(F)F)=C1)

`REAL300000042795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042795 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 40, 40, 65, 65, 65, 65, 65, 65, 65, 114, 114, 114, 114, 1, 1, 1, 1, 11, 40, 65, 65, 65, 1] 114
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042795 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2OC(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [65, 65, 65, 65, 65, 65, 65, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 65, 65, 65, 65, 25, 4, 1, 1, 1, 65] 114
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 165
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042795 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042795
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042795/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042795
Building REAL300000042796
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042796'
/scratch/stefan/7769623/working/building/REAL300000042796 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042796

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042796/0 /scratch/stefan/7769623/working/building/REAL300000042796 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/872
`/scratch/stefan/7769623/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042796 none CC(C)OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 128, 128, 128, 128, 128, 128, 128, 128, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 12, 44, 128, 128, 128, 128] 175
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 287
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042796 none CC(C)OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 128, 128, 128, 70, 128, 128, 128, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 175, 175, 175, 175, 175, 175, 175, 128, 128, 128, 57, 11, 1, 1, 1, 1] 175
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 522
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042796 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042796
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042796/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042796
Building REAL300000042797
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042797'
/scratch/stefan/7769623/working/building/REAL300000042797 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042797

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042797/0 /scratch/stefan/7769623/working/building/REAL300000042797 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/873
`/scratch/stefan/7769623/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC(F)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042797 none CCOC1=CC(F)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 64, 145, 145, 145, 145, 145, 145, 145, 144, 1, 15, 15, 15, 15, 15, 1, 1, 10, 64, 145, 145, 145, 144, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 27, 28] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 309
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042797 none CCOC1=CC(F)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 144, 144, 144, 144, 145, 144, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 144, 201, 201, 201, 201, 201, 144, 145, 55, 12, 1, 1, 1, 1, 144] 201
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 320
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042797 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042797
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042797/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042797
Building REAL300000042798
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042798'
/scratch/stefan/7769623/working/building/REAL300000042798 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042798

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042798/0 /scratch/stefan/7769623/working/building/REAL300000042798 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/874
`/scratch/stefan/7769623/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)=C1)

`REAL300000042798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042798 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 4, 19, 19, 27, 27, 19, 19, 47, 47, 47, 47, 47, 47, 27, 27, 1, 1, 1, 1, 4, 19, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 27, 27, 1] 47
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 155
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042798 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 44, 21, 21, 6, 6, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 15, 15, 47, 47, 47, 47, 44, 21, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 47] 47
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42])
total number of confs: 145
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042798 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 26, 27, 27, 15, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 1, 1, 27, 26, 27, 27, 15, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 27] 47
rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42])
total number of confs: 90
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042798 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042798
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042798/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042798
Building REAL300000042799
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042799'
/scratch/stefan/7769623/working/building/REAL300000042799 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042799

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042799/0 /scratch/stefan/7769623/working/building/REAL300000042799 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/875
`/scratch/stefan/7769623/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC(F)F)C=C2F)=C1)

`REAL300000042799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042799 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC(F)F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 57, 57, 39, 57, 181, 201, 201, 57, 57, 57, 1, 1, 1, 1, 9, 39, 57, 57, 201, 57, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 447
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042799 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OC(F)F)C=C2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 56, 57, 57, 24, 7, 7, 1, 1, 1, 1, 1, 1, 12, 44, 44, 1, 1, 1, 57, 56, 57, 57, 24, 7, 1, 1, 44, 1, 57] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 32, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042799 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042799
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042799/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042799
Building REAL300000042800
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042800'
/scratch/stefan/7769623/working/building/REAL300000042800 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042800

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042800/0 /scratch/stefan/7769623/working/building/REAL300000042800 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/876
`/scratch/stefan/7769623/working/3D/876' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042800 none CC(C)(C)OC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [8, 4, 8, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 52, 80, 80, 80, 80, 80, 80, 80, 80, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 10, 52, 80, 80, 80, 80, 1] 136
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 22, 41] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 187
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042800 none CC(C)(C)OC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 108, 136, 136, 80, 80, 79, 80, 80, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 136, 136, 136, 136, 136, 136, 136, 136, 136, 79, 80, 80, 32, 8, 1, 1, 1, 1, 80] 136
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41])
total number of confs: 351
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042800 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042800
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042800/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042800
Building REAL300000042801
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042801'
/scratch/stefan/7769623/working/building/REAL300000042801 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042801

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042801/0 /scratch/stefan/7769623/working/building/REAL300000042801 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/877
`/scratch/stefan/7769623/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1C)

`REAL300000042801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042801 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [3, 1, 1, 1, 1, 1, 8, 8, 30, 58, 58, 57, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 4, 4, 4, 1, 8, 30, 58, 58, 57, 58, 1, 2, 2, 2] 58
rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042801 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(F)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [58, 58, 58, 58, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 39, 11, 1, 1, 1, 1, 58, 58, 58, 58] 58
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042801 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042801
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042801/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042801
Building REAL300000042802
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042802'
/scratch/stefan/7769623/working/building/REAL300000042802 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042802

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042802/0 /scratch/stefan/7769623/working/building/REAL300000042802 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/878
`/scratch/stefan/7769623/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1Br)

`REAL300000042802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042802 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 44, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 44, 53, 53, 53, 53, 2, 2, 2] 53
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042802 none CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 43, 13, 1, 1, 1, 1, 53, 53, 53] 53
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042802 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042802
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042802/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042802
Building REAL300000042803
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042803'
/scratch/stefan/7769623/working/building/REAL300000042803 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042803

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042803/0 /scratch/stefan/7769623/working/building/REAL300000042803 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/879
`/scratch/stefan/7769623/working/3D/879' -> `0.mol2'
Preparing input files

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

`REAL300000042803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042803 none CC(CC1=CC=C(F)C=C1[N+](=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 55, 55, 86, 86, 86, 86, 86, 86, 86, 86, 11, 11, 11, 11, 6, 6, 1, 1, 1, 86, 86, 86, 86] 86
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 158
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042803 none CC(CC1=CC=C(F)C=C1[N+](=O)[O-])N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [41, 8, 41, 72, 86, 86, 85, 85, 86, 86, 86, 86, 86, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 72, 72, 86, 86, 86, 1, 1, 1, 1] 86
rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 313
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042803 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042803
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042803/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042803
Building REAL300000042804
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042804'
/scratch/stefan/7769623/working/building/REAL300000042804 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042804

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042804/0 /scratch/stefan/7769623/working/building/REAL300000042804 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/880
`/scratch/stefan/7769623/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=NN=CN2CC2=CC=CC=C2)=C1)

`REAL300000042804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042804 none O=C([O-])C1=CC=CC(N=NCC2=NN=CN2CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 90, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 47, 48, 90, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 718
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: REAL300000042804 none O=C([O-])C1=CC=CC(N=NCC2=NN=CN2CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 164, 164, 44, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 44, 44, 14, 5, 5, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37])
total number of confs: 379
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042804 none O=C([O-])C1=CC=CC(N=NCC2=NN=CN2CC2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 8, 14, 14, 90, 90, 90, 90, 7, 7, 1, 8, 8, 14, 14, 8, 14, 14, 90] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 181
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042804 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042804
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042804/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042804
Building REAL300000042805
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042805'
/scratch/stefan/7769623/working/building/REAL300000042805 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042805

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042805/0 /scratch/stefan/7769623/working/building/REAL300000042805 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/881
`/scratch/stefan/7769623/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=CC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CN=C12)

`REAL300000042805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042805 none COC(=O)C1=CC=CC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 54, 112, 112, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 12, 54, 112, 112, 112, 112, 1, 1] 169
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 22, 23, 24, 25, 38, 29, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042805 none COC(=O)C1=CC=CC2=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=CN=C12 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 169, 112, 169, 112, 112, 112, 112, 112, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 112, 112, 112, 112, 169, 169, 169, 112, 112, 112, 42, 12, 1, 1, 1, 1, 112, 112] 169
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 356
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042805 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042805
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042805/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042805
Building REAL300000042806
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042806'
/scratch/stefan/7769623/working/building/REAL300000042806 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042806

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042806/0 /scratch/stefan/7769623/working/building/REAL300000042806 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/882
`/scratch/stefan/7769623/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)=C1)

`REAL300000042806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042806 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 28, 28, 18, 18, 73, 88, 140, 201, 201, 201, 201, 201, 28, 28, 1, 1, 1, 1, 5, 18, 28, 28, 86, 86, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 28, 28, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 48, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 577
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: REAL300000042806 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 167, 98, 98, 45, 26, 59, 59, 26, 8, 5, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201, 201, 201, 201, 167, 98, 59, 59, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 201] 201
rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48])
total number of confs: 639
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042806 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(OCCN3CCOCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 12, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 19, 38, 59, 59, 59, 59, 59, 1, 1, 28, 28, 28, 28, 12, 3, 1, 1, 19, 19, 38, 38, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 28] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 46, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48])
total number of confs: 234
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042806 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042806
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042806/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042806
Building REAL300000042807
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042807'
/scratch/stefan/7769623/working/building/REAL300000042807 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042807

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042807/0 /scratch/stefan/7769623/working/building/REAL300000042807 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/883
`/scratch/stefan/7769623/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=C2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CNC2=CC=C1)

`REAL300000042807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042807 none N#CC1=C2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CNC2=CC=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 23, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 7, 23, 34, 34, 34, 34, 1, 1, 1, 1, 1] 34
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 20, 21, 22, 33, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042807 none N#CC1=C2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CNC2=CC=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 34, 34, 34, 31, 11, 1, 1, 1, 1, 34, 34, 34, 34, 34] 34
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33])
total number of confs: 61
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042807 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042807
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042807/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042807
Building REAL300000042808
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042808'
/scratch/stefan/7769623/working/building/REAL300000042808 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042808

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042808/0 /scratch/stefan/7769623/working/building/REAL300000042808 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/884
`/scratch/stefan/7769623/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC3=C(F)C=C(Cl)C=C23)=C1)

`REAL300000042808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042808 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=C(F)C=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 49, 49, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 13, 49, 81, 81, 81, 81, 1] 81
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042808 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=C(F)C=C(Cl)C=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 50, 10, 1, 1, 1, 1, 81] 81
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 24, 25, 26, 27])
total number of confs: 170
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042808 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042808
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042808/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042808
Building REAL300000042809
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042809'
/scratch/stefan/7769623/working/building/REAL300000042809 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042809

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042809/0 /scratch/stefan/7769623/working/building/REAL300000042809 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/885
`/scratch/stefan/7769623/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1=C2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CNC2=CC=C1)

`REAL300000042809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042809 none CC(C)(C)OC(=O)NC1=C2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CNC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 6
rigid atoms, others: [7, 8, 9, 10, 11, 45, 46, 47, 48, 49, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 25
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042809 none CC(C)(C)OC(=O)NC1=C2C(C=NNC3=CC=CC(C(=O)[O-])=C3)=CNC2=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 5, 6, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5] 6
rigid atoms, others: [41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042809 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042809
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042809/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042809
Building REAL300000042810
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042810'
/scratch/stefan/7769623/working/building/REAL300000042810 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042810

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042810/0 /scratch/stefan/7769623/working/building/REAL300000042810 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/886
`/scratch/stefan/7769623/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC1=CN=CC2=CC=CC=C21)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042810 none CC(CCC1=CN=CC2=CC=CC=C21)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 33, 33, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 38, 37] set([0, 1, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42])
total number of confs: 380
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042810 none CC(CCC1=CN=CC2=CC=CC=C21)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 48, 113, 131, 201, 201, 201, 201, 201, 201, 201, 201, 197, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 48, 48, 48, 121, 121, 126, 131, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 657
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042810 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042810
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042810/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042810
Building REAL300000042811
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042811'
/scratch/stefan/7769623/working/building/REAL300000042811 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042811

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042811/0 /scratch/stefan/7769623/working/building/REAL300000042811 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/887
`/scratch/stefan/7769623/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)C=CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C)

`REAL300000042811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042811 none CCOC(=O)C=CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 66, 52, 10, 52, 10, 1, 1, 1, 1, 1, 1, 8, 8, 21, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 106, 106, 106, 106, 106, 10, 10, 1, 1, 8, 21, 30, 30, 30, 30, 2, 2, 2] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 426
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042811 none CCOC(=O)C=CC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 194, 99, 194, 99, 30, 30, 30, 30, 21, 21, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 201, 201, 201, 201, 201, 99, 99, 30, 30, 21, 4, 1, 1, 1, 1, 30, 30, 30] 201
rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 575
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042811 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042811
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042811/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042811
Building REAL300000042812
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042812'
/scratch/stefan/7769623/working/building/REAL300000042812 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042812

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042812/0 /scratch/stefan/7769623/working/building/REAL300000042812 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/888
`/scratch/stefan/7769623/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1)

`REAL300000042812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042812 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 51, 9, 51, 1, 1, 1, 1, 1, 3, 3, 12, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 4, 4, 1, 4, 4, 1, 87, 87, 87, 87, 87, 9, 9, 1, 3, 12, 17, 17, 17, 17, 4, 4, 1, 4, 4] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 21, 22, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 366
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042812 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 96, 95, 19, 95, 4, 4, 4, 4, 4, 5, 5, 21, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 4, 136, 136, 136, 136, 136, 19, 19, 4, 5, 21, 28, 28, 28, 28, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 534
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042812 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 146, 145, 42, 145, 17, 17, 17, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 28, 28, 17, 28, 28, 17, 201, 201, 201, 201, 201, 42, 42, 17, 16, 4, 1, 1, 1, 1, 28, 28, 17, 28, 28] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47])
total number of confs: 769
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042812 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042812
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042812/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042812
Building REAL300000042813
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042813'
/scratch/stefan/7769623/working/building/REAL300000042813 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042813

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042813/0 /scratch/stefan/7769623/working/building/REAL300000042813 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/889
`/scratch/stefan/7769623/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCC3=CC=CC4=CC=CC2=C43)=C1)

`REAL300000042813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042813 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=CC4=CC=CC2=C43)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 24
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 44
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042813 none O=C([O-])C1=CC=CC(NN=C2CCC3=CC=CC4=CC=CC2=C43)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24] 24
rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 38, 23, 24, 25, 26, 27])
total number of confs: 40
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042813 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042813
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042813/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042813
Building REAL300000042814
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042814'
/scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300000042814

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042814/0 /scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/890
`/scratch/stefan/7769623/working/3D/890' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCN3CCSCC23)=C1)

`REAL300000042814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042814 none O=C([O-])C1=CC=CC(N=NC2CCCN3CCSCC23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 10, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 10
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042814 none O=C([O-])C1=CC=CC(N=NC2CCCN3CCSCC23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 10, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 10
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 38])
total number of confs: 14
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042814/1 /scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/891
`/scratch/stefan/7769623/working/3D/891' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC[N@@H+]3CCSCC23)=C1)

`REAL300000042814.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042814/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042814 none O=C([O-])C1=CC=CC(N=NC2CCC[N@@H+]3CCSCC23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042814 none O=C([O-])C1=CC=CC(N=NC2CCC[N@@H+]3CCSCC23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `2'
/scratch/stefan/7769623/working/building/REAL300000042814/2 /scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 2 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/892
`/scratch/stefan/7769623/working/3D/892' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC[N@H+]3CCSCC23)=C1)

`REAL300000042814.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300000042814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042814/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042814 none O=C([O-])C1=CC=CC(N=NC2CCC[N@H+]3CCSCC23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042814 none O=C([O-])C1=CC=CC(N=NC2CCC[N@H+]3CCSCC23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 9, 6, 5, 5, 14, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 23, 24])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042814 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042814
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
2: /scratch/stefan/7769623/working/building/REAL300000042814/2.*
0: /scratch/stefan/7769623/working/building/REAL300000042814/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042814/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042814
Building REAL300000042815
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042815'
/scratch/stefan/7769623/working/building/REAL300000042815 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042815

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042815/0 /scratch/stefan/7769623/working/building/REAL300000042815 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/893
`/scratch/stefan/7769623/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2C3=CC=CC=C3OCC2F)=C1)

`REAL300000042815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042815 none O=C([O-])C1=CC=CC(NN=C2C3=CC=CC=C3OCC2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 31
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042815 none O=C([O-])C1=CC=CC(NN=C2C3=CC=CC=C3OCC2F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 17] 17
rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 33])
total number of confs: 33
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042815 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042815
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042815/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042815
Building REAL300000042816
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042816'
/scratch/stefan/7769623/working/building/REAL300000042816 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042816

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042816/0 /scratch/stefan/7769623/working/building/REAL300000042816 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/894
`/scratch/stefan/7769623/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCCO3)N=N2)=C1)

`REAL300000042816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042816 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCCO3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 72, 72, 72, 165, 201, 201, 201, 201, 72, 72, 1, 1, 1, 1, 28, 29, 72, 165, 165, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 704
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042816 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCCO3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 176, 176, 54, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 18, 18, 201, 201, 201, 201, 54, 54, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 391
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042816 none O=C([O-])C1=CC=CC(N=NCC2=CN(CC3CCCO3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 40, 40, 6, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 1, 1, 72, 72, 72, 72, 6, 6, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18, 72] 201
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042816 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042816/1 /scratch/stefan/7769623/working/building/REAL300000042816 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/895
`/scratch/stefan/7769623/working/3D/895' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCCO3)N=N2)=C1)

`REAL300000042816.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042816/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042816 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCCO3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 48, 48, 48, 146, 201, 201, 201, 201, 48, 48, 1, 1, 1, 1, 9, 37, 48, 146, 146, 201, 201, 201, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 654
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042816 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCCO3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 156, 53, 53, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 156, 53, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38])
total number of confs: 473
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042816 none O=C([O-])C1=CC=CC(NN=CC2=CN(CC3CCCO3)N=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 22, 6, 6, 1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 1, 1, 48, 48, 48, 48, 22, 6, 1, 9, 9, 35, 35, 35, 35, 35, 35, 35, 48] 201
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 183
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042816 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042816
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042816/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042816/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042816
Building REAL300000042817
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042817'
/scratch/stefan/7769623/working/building/REAL300000042817 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042817

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042817/0 /scratch/stefan/7769623/working/building/REAL300000042817 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/896
`/scratch/stefan/7769623/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(CC=CN=NC2=CC=CC(C(=O)[O-])=C2)C=C1C)

`REAL300000042817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042817 none CC1=CC(C)=C(CC=CN=NC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 6, 39, 39, 129, 129, 189, 189, 189, 189, 189, 189, 189, 189, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6, 39, 39, 189, 189, 189, 189, 1, 2, 2, 2] 189
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 38] set([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, 39, 40, 41])
total number of confs: 340
number of broken/clashed sets: 148
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042817 none CC1=CC(C)=C(CC=CN=NC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [180, 177, 189, 183, 189, 139, 51, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 139, 139, 51, 51, 1, 1, 1, 1, 189, 189, 189, 189] 189
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 657
number of broken/clashed sets: 148
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042817 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042817
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042817/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042817
Building REAL300000042818
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042818'
/scratch/stefan/7769623/working/building/REAL300000042818 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042818

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042818/0 /scratch/stefan/7769623/working/building/REAL300000042818 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/897
`/scratch/stefan/7769623/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC(F)=CC=C2F)=N1)

`REAL300000042818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042818 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 13, 13, 52, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 11, 11, 11, 10, 11, 11, 11, 1, 2, 2, 2, 1, 13, 52, 91, 91, 91, 91, 11, 10, 11] 160
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042818 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [11, 11, 11, 11, 11, 46, 46, 134, 160, 160, 160, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 46, 134, 160, 160, 160, 160, 1, 1, 1] 160
rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 388
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042818 none CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC(F)=CC=C2F)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [91, 91, 91, 31, 31, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 91, 91, 160, 160, 160, 160, 160, 160, 160, 91, 91, 91, 91, 91, 31, 6, 1, 1, 1, 1, 160, 160, 160] 160
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042818 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042818
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042818/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042818
Building REAL300000042819
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042819'
/scratch/stefan/7769623/working/building/REAL300000042819 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042819

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042819/0 /scratch/stefan/7769623/working/building/REAL300000042819 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/898
`/scratch/stefan/7769623/working/3D/898' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2CCC2)C=C1)

`REAL300000042819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042819 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 88, 88, 53, 58, 166, 166, 166, 88, 88, 45, 45, 45, 10, 1, 1, 1, 1, 88, 88, 166, 166, 166, 166, 166, 166, 166, 88, 88] 166
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 537
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: REAL300000042819 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [19, 1, 18, 18, 95, 166, 166, 166, 166, 166, 166, 166, 166, 1, 7, 7, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 95, 166, 166, 166, 166, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7] 166
rigid atoms, others: [34, 35, 36, 37, 38, 33, 39, 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, 32, 40, 41])
total number of confs: 353
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042819 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 37, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 6, 6, 6, 37, 88, 88, 88, 88, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1] 166
rigid atoms, others: [32, 1, 40, 41, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 173
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042819 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042819
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042819/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042819
Building REAL300000042820
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042820'
/scratch/stefan/7769623/working/building/REAL300000042820 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042820

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042820/0 /scratch/stefan/7769623/working/building/REAL300000042820 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/899
`/scratch/stefan/7769623/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=CC=CC(F)=C3N=C2)=C1)

`REAL300000042820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042820 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC=CC(F)=C3N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 44, 44, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 13, 44, 71, 71, 71, 71, 71, 1] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 122
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042820 none O=C([O-])C1=CC=CC(NN=CC2=CC3=CC=CC(F)=C3N=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 70, 71, 71, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 70, 71, 71, 47, 8, 1, 1, 1, 1, 1, 71] 71
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 22, 23, 24, 25, 26, 27])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042820 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042820
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042820/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042820
Building REAL300000042821
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042821'
/scratch/stefan/7769623/working/building/REAL300000042821 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042821

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042821/0 /scratch/stefan/7769623/working/building/REAL300000042821 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/900
`/scratch/stefan/7769623/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CSC(CN=NC2=CC=CC(C(=O)[O-])=C2)=N1)

`REAL300000042821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042821 none CC(C)(C)C1=CSC(CN=NC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 65, 66, 144, 144, 144, 144, 144, 144, 144, 144, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 8, 8, 144, 144, 144, 144] 201
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 228
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042821 none CC(C)(C)C1=CSC(CN=NC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 143, 201, 201, 143, 143, 143, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 42, 42, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 618
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042821 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042821/1 /scratch/stefan/7769623/working/building/REAL300000042821 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/901
`/scratch/stefan/7769623/working/3D/901' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=CSC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1)

`REAL300000042821.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042821/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042821 none CC(C)(C)C1=CSC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 8, 36, 61, 61, 61, 61, 61, 61, 61, 61, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 8, 35, 61, 61, 61, 60] 75
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 133
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042821 none CC(C)(C)C1=CSC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 61, 75, 75, 60, 60, 61, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 60, 75, 75, 75, 75, 75, 75, 75, 75, 75, 60, 38, 10, 1, 1, 1, 1] 75
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 189
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042821 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042821
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042821/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042821/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042821
Building REAL300000042822
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042822'
/scratch/stefan/7769623/working/building/REAL300000042822 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042822

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042822/0 /scratch/stefan/7769623/working/building/REAL300000042822 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/902
`/scratch/stefan/7769623/working/3D/902' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(CC=CN=NC2=CC=CC(C(=O)[O-])=C2)C(C)=C1)

`REAL300000042822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042822 none CC1=CC(C)=C(CC=CN=NC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 38, 38, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 3, 11, 11, 46, 46, 46, 46, 2, 2, 2, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 20, 21, 22, 26] set([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, 39, 40])
total number of confs: 98
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042822 none CC1=CC(C)=C(CC=CN=NC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 30, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 30, 30, 1, 1, 1, 1, 44, 44, 44, 44] 44
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 139
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042822 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042822
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042822/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042822
Building REAL300000042823
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042823'
/scratch/stefan/7769623/working/building/REAL300000042823 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042823

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042823/0 /scratch/stefan/7769623/working/building/REAL300000042823 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/903
`/scratch/stefan/7769623/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042823 none COCCC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 8, 1, 1, 1, 1, 1, 1, 6, 6, 33, 75, 75, 75, 75, 75, 76, 76, 75, 1, 43, 43, 43, 14, 14, 8, 8, 1, 6, 33, 75, 75, 75, 75] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 246
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042823 none COCCC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 173, 75, 75, 75, 75, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 201, 201, 201, 200, 200, 173, 173, 75, 37, 8, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042823 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042823
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042823/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042823
Building REAL300000042824
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042824'
/scratch/stefan/7769623/working/building/REAL300000042824 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042824

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042824/0 /scratch/stefan/7769623/working/building/REAL300000042824 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/904
`/scratch/stefan/7769623/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1S(=O)(=O)N(C)C)

`REAL300000042824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042824 none CCC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1S(=O)(=O)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 14, 11, 11, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 9, 9, 40, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 10, 10, 10, 16, 16, 6, 6, 6, 6, 6, 1, 9, 40, 92, 92, 92, 92, 16, 16, 16, 16, 16, 16] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042824 none CCC1=NC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1S(=O)(=O)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 14, 11, 11, 8, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 92, 92, 92, 92, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 92, 92, 176, 176, 176, 185, 185, 146, 146, 146, 146, 146, 92, 31, 7, 1, 1, 1, 1, 185, 185, 185, 185, 185, 185] 201
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 833
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042824 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042824
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042824/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042824
Building REAL300000042825
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042825'
/scratch/stefan/7769623/working/building/REAL300000042825 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042825

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042825/0 /scratch/stefan/7769623/working/building/REAL300000042825 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/905
`/scratch/stefan/7769623/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Br)

`REAL300000042825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042825 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 11, 11, 69, 160, 160, 160, 160, 160, 160, 160, 160, 1, 1, 1, 7, 7, 7, 1, 1, 11, 69, 160, 160, 160, 160, 1] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042825 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 159, 201, 159, 160, 160, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 160, 160, 160, 201, 201, 201, 160, 160, 60, 12, 1, 1, 1, 1, 160] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 401
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042825 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042825
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042825/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042825
Building REAL300000042826
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042826'
/scratch/stefan/7769623/working/building/REAL300000042826 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042826

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042826/0 /scratch/stefan/7769623/working/building/REAL300000042826 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/906
`/scratch/stefan/7769623/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2[O-])=C1)

`REAL300000042826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042826 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 22
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042826 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 10, 4, 1, 1, 11] 11
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042826 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042826/1 /scratch/stefan/7769623/working/building/REAL300000042826 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/907
`/scratch/stefan/7769623/working/3D/907' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2O)=C1)

`REAL300000042826.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042826/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042826 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 10, 32, 34, 34, 68, 1] 68
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 122
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042826 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [34, 34, 34, 34, 34, 34, 34, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 24, 8, 1, 1, 2, 34] 68
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 80
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042826 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042826
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042826/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042826/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042826
Building REAL300000042827
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042827'
/scratch/stefan/7769623/working/building/REAL300000042827 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042827

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042827/0 /scratch/stefan/7769623/working/building/REAL300000042827 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/908
`/scratch/stefan/7769623/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(F)=C2[O-])=C1)

`REAL300000042827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042827 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(F)=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 22
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042827 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(F)=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 10, 4, 1, 1, 11] 11
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042827 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042827/1 /scratch/stefan/7769623/working/building/REAL300000042827 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/909
`/scratch/stefan/7769623/working/3D/909' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(F)=C2O)=C1)

`REAL300000042827.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042827/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042827 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(F)=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 11, 31, 33, 33, 66, 1] 66
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28])
total number of confs: 120
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042827 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC(F)=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 15, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 24, 8, 1, 1, 2, 33] 66
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 79
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042827 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042827
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042827/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042827/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042827
Building REAL300000042828
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042828'
/scratch/stefan/7769623/working/building/REAL300000042828 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042828

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042828/0 /scratch/stefan/7769623/working/building/REAL300000042828 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/910
`/scratch/stefan/7769623/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1C)

`REAL300000042828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042828 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 65, 65, 55, 48, 65, 65, 65, 49, 49, 49, 10, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65] 65
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 141
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042828 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(Br)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [9, 1, 9, 9, 45, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 65, 65, 65, 65, 1, 1, 1, 2, 2, 2] 65
rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34])
total number of confs: 149
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042828 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042828
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042828/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042828
Building REAL300000042829
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042829'
/scratch/stefan/7769623/working/building/REAL300000042829 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042829

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042829/0 /scratch/stefan/7769623/working/building/REAL300000042829 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/911
`/scratch/stefan/7769623/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1)

`REAL300000042829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042829 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 71, 71, 50, 71, 71, 71, 118, 201, 201, 201, 201, 201, 201, 27, 27, 27, 7, 1, 1, 1, 1, 71, 71, 71, 71, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042829 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 27, 95, 95, 173, 201, 201, 201, 201, 201, 201, 201, 201, 27, 27, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 173, 201, 201, 201, 201, 27, 27, 27, 27, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 483
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042829 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1OC1=CC=CC(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 30, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 9, 9, 9, 30, 71, 71, 71, 71, 1, 1, 1, 1, 27, 27, 27, 27] 201
rigid atoms, others: [1, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42])
total number of confs: 169
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042829 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042829
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042829/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042829
Building REAL300000042830
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042830'
/scratch/stefan/7769623/working/building/REAL300000042830 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042830

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042830/0 /scratch/stefan/7769623/working/building/REAL300000042830 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/912
`/scratch/stefan/7769623/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1)

`REAL300000042830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042830 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 76, 76, 76, 57, 76, 76, 76, 127, 201, 201, 201, 201, 201, 201, 25, 25, 25, 6, 1, 1, 1, 1, 76, 43, 76, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 390
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: REAL300000042830 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 27, 90, 90, 175, 201, 201, 201, 201, 201, 201, 201, 201, 27, 27, 26, 26, 27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 175, 201, 201, 201, 201, 27, 27, 27, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 497
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042830 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=CC(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 37, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 9, 9, 9, 37, 76, 76, 76, 76, 1, 1, 1, 27, 27, 27, 27] 201
rigid atoms, others: [1, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42])
total number of confs: 185
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042830 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042830
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042830/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042830
Building REAL300000042831
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042831'
/scratch/stefan/7769623/working/building/REAL300000042831 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042831

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042831/0 /scratch/stefan/7769623/working/building/REAL300000042831 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/913
`/scratch/stefan/7769623/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C2CCCC3=C2C=NN3CCO)=C1)

`REAL300000042831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042831 none O=C([O-])C1=CC=CC(NN=C2CCCC3=C2C=NN3CCO)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 67, 67, 1, 1, 1, 1, 11, 32, 32, 32, 32, 32, 32, 32, 67, 67, 67, 67, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 425
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042831 none O=C([O-])C1=CC=CC(NN=C2CCCC3=C2C=NN3CCO)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 8, 8, 5, 5, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 32, 32, 32, 32, 32, 32, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 32, 32, 32, 32, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 30, 32] 201
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 39, 34, 35, 20, 21, 22, 23, 24, 25, 26, 38, 37, 36])
total number of confs: 114
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042831 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042831
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042831/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042831
Building REAL300000042832
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042832'
/scratch/stefan/7769623/working/building/REAL300000042832 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042832

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042832/0 /scratch/stefan/7769623/working/building/REAL300000042832 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/914
`/scratch/stefan/7769623/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CS1)

`REAL300000042832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042832 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [93, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 141, 141, 141, 141, 141, 96, 96, 96, 95, 95, 10, 1, 1, 1, 1, 141, 141] 152
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 456
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042832 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [30, 9, 1, 9, 9, 61, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 31, 31, 31, 30, 30, 61, 141, 141, 141, 141, 1, 1] 152
rigid atoms, others: [2, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 363
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042832 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042832/1 /scratch/stefan/7769623/working/building/REAL300000042832 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/915
`/scratch/stefan/7769623/working/3D/915' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CS1)

`REAL300000042832.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042832/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042832 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [65, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 94, 94, 94, 94, 94, 72, 72, 72, 72, 72, 45, 1, 1, 1, 1, 94, 94] 106
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 404
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042832 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=C(Cl)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 8, 1, 8, 40, 40, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 8, 94, 94, 94, 94, 1, 1] 106
rigid atoms, others: [2, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042832 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042832
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042832/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042832/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042832
Building REAL300000042833
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042833'
/scratch/stefan/7769623/working/building/REAL300000042833 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042833

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042833/0 /scratch/stefan/7769623/working/building/REAL300000042833 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/916
`/scratch/stefan/7769623/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)=C1)

`REAL300000042833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042833 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 9, 38, 54, 54, 54, 1] 54
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 84
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042833 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=CC(F)=C(F)C(F)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 40, 10, 1, 1, 1, 54] 54
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042833 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042833
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042833/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042833
Building REAL300000042834
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042834'
/scratch/stefan/7769623/working/building/REAL300000042834 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042834

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042834/0 /scratch/stefan/7769623/working/building/REAL300000042834 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/917
`/scratch/stefan/7769623/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)=C1)

`REAL300000042834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042834 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 11, 37, 53, 53, 53, 1] 53
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042834 none O=C([O-])C1=CC=CC(NN=CC2=CNC3=C(F)C=C(F)C(F)=C23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 15, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 39, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 39, 10, 1, 1, 1, 53] 53
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042834 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042834
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042834/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042834
Building REAL300000042835
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042835'
/scratch/stefan/7769623/working/building/REAL300000042835 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042835

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042835/0 /scratch/stefan/7769623/working/building/REAL300000042835 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/918
`/scratch/stefan/7769623/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O)

`REAL300000042835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042835 none COC1=CC(C)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 4, 4, 4, 1, 2, 2, 2, 1, 9, 31, 65, 65, 65, 65, 2] 130
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 139
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042835 none COC1=CC(C)=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [65, 65, 65, 65, 65, 65, 65, 48, 48, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 48, 9, 1, 1, 1, 1, 130] 130
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 230
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042835 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042835
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042835/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042835
Building REAL300000042836
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042836'
/scratch/stefan/7769623/working/building/REAL300000042836 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042836

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042836/0 /scratch/stefan/7769623/working/building/REAL300000042836 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/919
`/scratch/stefan/7769623/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)=C1)

`REAL300000042836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042836 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 54, 54, 54, 52, 54, 54, 54, 101, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 28, 54, 33, 54, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([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: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042836 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 177, 85, 85, 29, 29, 29, 29, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 177, 85, 29, 29, 29, 1, 1, 1, 201] 201
rigid atoms, others: [35, 36, 37, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 514
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042836 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CN=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 8, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 53, 54, 54, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 29, 54, 53, 54, 54, 31, 10, 1, 1, 1, 29, 29, 29, 54] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042836 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042836
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042836/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042836
Building REAL300000042837
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042837'
/scratch/stefan/7769623/working/building/REAL300000042837 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042837

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042837/0 /scratch/stefan/7769623/working/building/REAL300000042837 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/920
`/scratch/stefan/7769623/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCOCC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042837 none CC(CCOCC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 67, 51, 15, 3, 1, 1, 1, 1, 1, 1, 1, 100, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 100, 67, 67, 51, 51, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41])
total number of confs: 638
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042837 none CC(CCOCC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 21, 32, 53, 101, 201, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 32, 32, 53, 53, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 802
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042837 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042837
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042837/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042837
Building REAL300000042838
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042838'
/scratch/stefan/7769623/working/building/REAL300000042838 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042838

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042838/0 /scratch/stefan/7769623/working/building/REAL300000042838 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/921
`/scratch/stefan/7769623/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042838 none CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 5, 5, 5, 9, 11, 11, 11, 11] 17
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 36
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042838 none CSC1=CC=C([N+](=O)[O-])C=C1C(C)=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1] 17
rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 35
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042838 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042838
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042838/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042838
Building REAL300000042839
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042839'
/scratch/stefan/7769623/working/building/REAL300000042839 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042839

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042839/0 /scratch/stefan/7769623/working/building/REAL300000042839 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/922
`/scratch/stefan/7769623/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCCC3=CC=CC=C3C2)=C1)

`REAL300000042839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042839 none O=C([O-])C1=CC=CC(N=NC2CCCCC3=CC=CC=C3C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 27
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042839 none O=C([O-])C1=CC=CC(N=NC2CCCCC3=CC=CC=C3C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 22, 23, 24, 25])
total number of confs: 20
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042839 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042839
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042839/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042839
Building REAL300000042840
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042840'
/scratch/stefan/7769623/working/building/REAL300000042840 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042840

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042840/0 /scratch/stefan/7769623/working/building/REAL300000042840 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/923
`/scratch/stefan/7769623/working/3D/923' -> `0.mol2'
Preparing input files

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

`REAL300000042840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042840 none CC(C)OCC(CC1=CC=C(F)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 83, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 28, 70, 70, 70, 70, 70, 70, 70, 70, 83, 83, 83, 83, 83, 83, 83, 23, 23, 6, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 39, 38, 37] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44])
total number of confs: 387
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042840 none CC(C)OCC(CC1=CC=C(F)C=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 154, 186, 91, 34, 6, 34, 70, 70, 70, 70, 70, 70, 70, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 186, 186, 186, 186, 186, 186, 186, 91, 91, 34, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1] 201
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 818
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042840 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042840
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042840/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042840
Building REAL300000042841
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042841'
/scratch/stefan/7769623/working/building/REAL300000042841 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042841

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042841/0 /scratch/stefan/7769623/working/building/REAL300000042841 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/924
`/scratch/stefan/7769623/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2NC(=O)C(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1OC)

`REAL300000042841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042841 none COC1=CC=C2NC(=O)C(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 36, 36, 36, 37, 37, 36, 1, 1, 1, 5, 4, 4, 4, 1, 1, 1, 7, 36, 36, 36, 36, 5, 5, 5] 46
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042841 none COC1=CC=C2NC(=O)C(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 45, 46, 46, 46, 36, 36, 36, 12, 1, 1, 1, 1, 45, 45, 45] 46
rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042841 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042841
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042841/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042841
Building REAL300000042842
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042842'
/scratch/stefan/7769623/working/building/REAL300000042842 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042842

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042842/0 /scratch/stefan/7769623/working/building/REAL300000042842 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/925
`/scratch/stefan/7769623/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C2CCSCC2=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042842 none CN1N=C2CCSCC2=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 14, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 56, 87, 87, 87, 87, 87, 87, 87, 87, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 55, 87, 87, 87, 87] 87
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31])
total number of confs: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042842 none CN1N=C2CCSCC2=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 14, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 86, 86, 86, 87, 87, 87, 87, 86, 45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 45, 12, 1, 1, 1, 1] 87
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042842 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042842
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042842/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042842
Building REAL300000042843
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042843'
/scratch/stefan/7769623/working/building/REAL300000042843 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042843

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042843/0 /scratch/stefan/7769623/working/building/REAL300000042843 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/926
`/scratch/stefan/7769623/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1)

`REAL300000042843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042843 none CCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 11, 11, 50, 116, 116, 116, 116, 116, 116, 116, 116, 1, 1, 6, 6, 1, 6, 6, 1, 9, 9, 9, 9, 9, 1, 11, 50, 116, 116, 116, 116, 6, 6, 2, 6, 6] 190
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 257
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: REAL300000042843 none CCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [33, 6, 6, 6, 6, 6, 32, 32, 100, 165, 165, 165, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 33, 33, 6, 32, 100, 165, 165, 165, 165, 1, 1, 1, 1, 1] 190
rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 443
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042843 none CCN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [184, 116, 116, 116, 42, 42, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 116, 116, 165, 165, 123, 165, 165, 116, 184, 184, 184, 184, 184, 116, 42, 9, 1, 1, 1, 1, 165, 165, 151, 165, 165] 190
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41])
total number of confs: 790
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042843 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042843
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042843/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042843
Building REAL300000042844
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042844'
/scratch/stefan/7769623/working/building/REAL300000042844 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042844

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042844/0 /scratch/stefan/7769623/working/building/REAL300000042844 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/927
`/scratch/stefan/7769623/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=C(C)C=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1C)

`REAL300000042844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042844 none COCC1=C(C)C=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 16, 16, 16, 6, 6, 2, 2, 2, 1, 2, 2, 2, 7, 35, 75, 75, 75, 75, 2, 2, 2] 121
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 191
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042844 none COCC1=C(C)C=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 5, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 75, 75, 32, 51, 75, 75, 75, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 75, 75, 121, 121, 121, 121, 121, 75, 75, 75, 75, 75, 75, 75, 32, 10, 1, 1, 1, 1, 75, 75, 75] 121
rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44])
total number of confs: 606
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042844 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042844
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042844/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042844
Building REAL300000042845
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042845'
/scratch/stefan/7769623/working/building/REAL300000042845 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042845

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042845/0 /scratch/stefan/7769623/working/building/REAL300000042845 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/928
`/scratch/stefan/7769623/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(Cl)=C2)=CC=C1F)

`REAL300000042845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042845 none CC1=CC(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(Cl)=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 79, 79, 163, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 79, 163, 201, 201, 201, 201, 37, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 518
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042845 none CC1=CC(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(Cl)=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 17, 16, 25, 25, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 16, 4, 1, 1, 1, 1, 25, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 345
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042845 none CC1=CC(OC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(Cl)=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 8, 1, 1, 1, 1, 1, 1, 4, 4, 12, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 37, 37, 21, 36, 37, 37, 37, 37, 1, 1, 4, 12, 25, 25, 25, 25, 1, 37, 37] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 40, 21, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042845 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042845
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042845/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042845
Building REAL300000042846
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042846'
/scratch/stefan/7769623/working/building/REAL300000042846 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042846

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042846/0 /scratch/stefan/7769623/working/building/REAL300000042846 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/929
`/scratch/stefan/7769623/working/3D/929' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1)

`REAL300000042846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042846 none CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 55, 55, 128, 163, 163, 163, 163, 163, 163, 163, 163, 19, 19, 19, 5, 5, 5, 5, 5, 1, 1, 1, 1, 19, 19, 55, 128, 163, 163, 163, 163, 19] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
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: REAL300000042846 none CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 163, 163, 163, 129, 163, 163, 104, 25, 24, 30, 30, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 30, 201, 201, 201, 201, 201, 163, 135, 163, 163, 30, 30, 21, 6, 1, 1, 1, 1, 30] 201
rigid atoms, others: [41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45])
total number of confs: 592
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042846 none CCC1=CC=CC=C1OC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 19, 19, 19, 14, 19, 18, 9, 1, 1, 1, 1, 1, 1, 4, 4, 15, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 37, 37, 37, 37, 37, 19, 15, 18, 19, 1, 1, 4, 15, 30, 30, 30, 30, 1] 201
rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 13, 45, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042846 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042846
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042846/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042846
Building REAL300000042847
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042847'
/scratch/stefan/7769623/working/building/REAL300000042847 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042847

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042847/0 /scratch/stefan/7769623/working/building/REAL300000042847 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/930
`/scratch/stefan/7769623/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)=C1)

`REAL300000042847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042847 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 61, 61, 61, 61, 61, 61, 102, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 29, 61, 61, 61, 61, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([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: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042847 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 173, 86, 86, 31, 31, 31, 31, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 173, 86, 31, 31, 31, 31, 1, 1, 1, 201] 201
rigid atoms, others: [36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 499
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042847 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=C(F)C(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 35, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 31, 61, 61, 61, 61, 35, 11, 1, 1, 1, 1, 31, 31, 31, 61] 201
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39])
total number of confs: 160
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042847 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042847
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042847/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042847
Building REAL300000042848
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042848'
/scratch/stefan/7769623/working/building/REAL300000042848 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042848

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042848/0 /scratch/stefan/7769623/working/building/REAL300000042848 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/931
`/scratch/stefan/7769623/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042848 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 55, 55, 124, 146, 146, 146, 146, 146, 146, 146, 146, 2, 2, 2, 1, 1, 1, 15, 15, 15, 55, 124, 146, 146, 146, 146] 146
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 357
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: REAL300000042848 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 133, 144, 146, 146, 133, 70, 70, 70, 44, 70, 70, 70, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 146, 146, 146, 146, 146, 146, 70, 44, 70, 35, 7, 1, 1, 1, 1] 146
rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 360
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042848 none CC1=CC(Cl)=CC=C1OC1=CC=C(F)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [15, 15, 15, 6, 9, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 39, 70, 70, 70, 70, 70, 70, 70, 70, 15, 15, 15, 15, 15, 15, 1, 1, 1, 13, 39, 70, 70, 70, 70] 146
rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42])
total number of confs: 187
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042848 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042848
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042848/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042848
Building REAL300000042849
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042849'
/scratch/stefan/7769623/working/building/REAL300000042849 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042849

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042849/0 /scratch/stefan/7769623/working/building/REAL300000042849 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/932
`/scratch/stefan/7769623/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F)

`REAL300000042849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042849 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 31, 31, 31, 19, 31, 31, 31, 81, 81, 173, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 81, 173, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042849 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 102, 52, 52, 52, 26, 52, 52, 52, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 102, 102, 201, 201, 201, 201, 52, 52, 52, 24, 7, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 694
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042849 none CC1=CC(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)=CC=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 52, 52, 52, 52, 52, 52, 52, 52, 31, 31, 8, 8, 31, 31, 31, 31, 1, 1, 1, 8, 26, 52, 52, 52, 52, 31, 31] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 176
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042849 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042849
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042849/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042849
Building REAL300000042850
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042850'
/scratch/stefan/7769623/working/building/REAL300000042850 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042850

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042850/0 /scratch/stefan/7769623/working/building/REAL300000042850 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/933
`/scratch/stefan/7769623/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042850 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 61, 61, 126, 146, 146, 146, 146, 146, 146, 146, 146, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 61, 126, 146, 146, 146, 146] 146
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 357
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: REAL300000042850 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 146, 146, 146, 129, 67, 67, 67, 41, 67, 67, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 146, 146, 146, 146, 146, 146, 67, 67, 67, 67, 32, 7, 1, 1, 1, 1] 146
rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 336
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042850 none CC1=CC=C(Cl)C=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 36, 67, 67, 67, 67, 67, 67, 67, 67, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 13, 36, 67, 67, 67, 67] 146
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 156
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042850 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042850
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042850/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042850
Building REAL300000042851
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042851'
/scratch/stefan/7769623/working/building/REAL300000042851 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042851

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042851/0 /scratch/stefan/7769623/working/building/REAL300000042851 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/934
`/scratch/stefan/7769623/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)=C1)

`REAL300000042851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042851 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 32, 32, 69, 69, 69, 63, 69, 69, 69, 113, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 32, 69, 69, 69, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([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: 340
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042851 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 182, 85, 85, 31, 31, 31, 30, 30, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 182, 85, 31, 31, 31, 1, 1, 1, 1, 201] 201
rigid atoms, others: [35, 36, 37, 38, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 512
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042851 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 31, 31, 69, 69, 69, 69, 37, 10, 1, 1, 1, 31, 31, 31, 31, 69] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 172
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042851 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042851
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042851/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042851
Building REAL300000042852
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042852'
/scratch/stefan/7769623/working/building/REAL300000042852 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042852

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042852/0 /scratch/stefan/7769623/working/building/REAL300000042852 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/935
`/scratch/stefan/7769623/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042852 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 51, 51, 120, 158, 158, 158, 158, 158, 158, 158, 158, 6, 6, 6, 6, 6, 1, 1, 1, 1, 13, 13, 13, 51, 120, 158, 158, 158, 158] 183
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 364
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: REAL300000042852 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [183, 158, 158, 158, 135, 158, 158, 135, 66, 66, 66, 34, 66, 66, 66, 30, 30, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 183, 183, 183, 183, 183, 158, 143, 158, 158, 66, 66, 66, 30, 5, 1, 1, 1, 1] 183
rigid atoms, others: [42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 601
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042852 none CCC1=CC=CC=C1OC1=CC=C(Cl)C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [34, 13, 13, 13, 6, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 35, 66, 66, 66, 66, 66, 66, 66, 66, 34, 34, 34, 34, 34, 13, 6, 13, 13, 1, 1, 1, 13, 35, 66, 66, 66, 66] 183
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45])
total number of confs: 253
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042852 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042852
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042852/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042852
Building REAL300000042853
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042853'
/scratch/stefan/7769623/working/building/REAL300000042853 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042853

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042853/0 /scratch/stefan/7769623/working/building/REAL300000042853 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/936
`/scratch/stefan/7769623/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042853 none CC1=C(Br)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 42, 52, 52, 52, 52, 52, 52, 52, 52, 1, 2, 2, 2, 1, 9, 42, 52, 52, 52, 52] 52
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042853 none CC1=C(Br)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 52, 52, 35, 35, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 52, 52, 52, 52, 35, 12, 1, 1, 1, 1] 52
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042853 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042853
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042853/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042853
Building REAL300000042854
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042854'
/scratch/stefan/7769623/working/building/REAL300000042854 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042854

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042854/0 /scratch/stefan/7769623/working/building/REAL300000042854 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/937
`/scratch/stefan/7769623/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC2=C(C=C1OC)C(=NNC1=CC=CC(C(=O)[O-])=C1)CCCC2)

`REAL300000042854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042854 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=CC(C(=O)[O-])=C1)CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 7, 46, 46, 46, 46, 46, 47, 47, 46, 1, 1, 1, 1, 3, 3, 3, 1, 1, 4, 4, 4, 7, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1] 72
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 22, 23, 24, 25, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 77
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042854 none COC1=CC2=C(C=C1OC)C(=NNC1=CC=CC(C(=O)[O-])=C1)CCCC2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [71, 46, 46, 46, 46, 46, 46, 46, 46, 72, 46, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 46, 46, 71, 71, 71, 46, 46, 72, 72, 72, 9, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46] 72
rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 169
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042854 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042854
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042854/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042854
Building REAL300000042855
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042855'
/scratch/stefan/7769623/working/building/REAL300000042855 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042855

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042855/0 /scratch/stefan/7769623/working/building/REAL300000042855 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/938
`/scratch/stefan/7769623/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)=C1)

`REAL300000042855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042855 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 65, 65, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 1, 1, 13, 65, 172, 172, 172, 172, 172, 172, 172, 172, 1] 172
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 248
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042855 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [172, 172, 172, 172, 172, 172, 172, 111, 19, 19, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 172, 172, 172, 172, 111, 19, 3, 3, 3, 1, 1, 1, 1, 3, 172] 172
rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 366
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042855 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(C3=CC=C(Cl)C=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [172, 172, 172, 172, 172, 172, 172, 69, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 172, 172, 172, 172, 69, 10, 1, 1, 1, 3, 3, 3, 3, 1, 172] 172
rigid atoms, others: [32, 37, 10, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38])
total number of confs: 312
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042855 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042855
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042855/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042855
Building REAL300000042856
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042856'
/scratch/stefan/7769623/working/building/REAL300000042856 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042856

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042856/0 /scratch/stefan/7769623/working/building/REAL300000042856 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/939
`/scratch/stefan/7769623/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2I)=C1)

`REAL300000042856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042856 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2I)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 35, 35, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 12, 35, 46, 46, 46, 1] 46
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 76
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042856 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(F)=C2I)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'I', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 18, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 35, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 35, 9, 1, 1, 1, 46] 46
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042856 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042856
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042856/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042856
Building REAL300000042857
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042857'
/scratch/stefan/7769623/working/building/REAL300000042857 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042857

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042857/0 /scratch/stefan/7769623/working/building/REAL300000042857 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/940
`/scratch/stefan/7769623/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C)

`REAL300000042857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042857 none CCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 7, 1, 1, 1, 1, 1, 1, 7, 7, 34, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 52, 52, 52, 52, 52, 28, 28, 1, 1, 7, 34, 66, 66, 66, 66, 1, 2, 2, 2] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 22, 38, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042857 none CCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 41, 40, 66, 66, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 201, 201, 201, 201, 201, 195, 197, 66, 66, 23, 5, 1, 1, 1, 1, 66, 66, 66, 66] 201
rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 624
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042857 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042857
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042857/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042857
Building REAL300000042858
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042858'
/scratch/stefan/7769623/working/building/REAL300000042858 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042858

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042858/0 /scratch/stefan/7769623/working/building/REAL300000042858 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/941
`/scratch/stefan/7769623/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1COC1=CC=CC=C1)

`REAL300000042858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042858 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1COC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 30, 66, 66, 66, 66, 66, 67, 67, 66, 1, 1, 1, 7, 9, 10, 10, 9, 10, 10, 4, 4, 4, 1, 1, 6, 30, 66, 66, 66, 66, 1, 7, 7, 10, 10, 9, 10, 10] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 39, 18, 19, 20, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 170
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: REAL300000042858 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1COC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 10, 10, 10, 10, 10, 10, 43, 43, 125, 201, 201, 201, 201, 201, 201, 201, 201, 10, 4, 2, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 10, 10, 43, 125, 201, 201, 201, 201, 10, 4, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [42, 43, 44, 45, 46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 461
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042858 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1COC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 44, 26, 66, 66, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 200, 200, 201, 201, 200, 201, 201, 130, 130, 130, 66, 66, 26, 6, 1, 1, 1, 1, 66, 200, 200, 201, 201, 200, 201, 201] 201
rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 909
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042858 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042858
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042858/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042858
Building REAL300000042859
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042859'
/scratch/stefan/7769623/working/building/REAL300000042859 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042859

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042859/0 /scratch/stefan/7769623/working/building/REAL300000042859 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/942
`/scratch/stefan/7769623/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1CN1C=CC=N1)

`REAL300000042859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042859 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1CN1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 6, 6, 27, 59, 59, 59, 59, 59, 60, 60, 59, 1, 1, 1, 8, 30, 30, 30, 30, 4, 4, 4, 1, 1, 6, 27, 59, 59, 60, 59, 1, 8, 8, 30, 30, 30] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 29, 30, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042859 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1CN1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 30, 30, 30, 30, 30, 30, 72, 72, 142, 201, 201, 201, 201, 201, 201, 201, 201, 30, 9, 1, 1, 1, 1, 1, 1, 47, 47, 47, 30, 30, 72, 142, 201, 201, 201, 201, 30, 9, 9, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 519
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042859 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1CN1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 59, 59, 59, 59, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 59, 59, 59, 128, 201, 201, 201, 201, 87, 87, 87, 59, 59, 30, 8, 1, 1, 1, 1, 59, 128, 128, 201, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42])
total number of confs: 576
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042859 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042859
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042859/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042859
Building REAL300000042860
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042860'
/scratch/stefan/7769623/working/building/REAL300000042860 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042860

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042860/0 /scratch/stefan/7769623/working/building/REAL300000042860 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/943
`/scratch/stefan/7769623/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=CC=CC(F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042860 none CCOC1=CC=CC(F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 78, 160, 160, 160, 160, 160, 161, 161, 160, 31, 31, 31, 30, 30, 1, 1, 1, 12, 78, 160, 160, 160, 160] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 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: 402
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042860 none CCOC1=CC=CC(F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 160, 160, 160, 93, 160, 160, 160, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 160, 160, 160, 50, 12, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 559
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042860 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042860
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042860/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042860
Building REAL300000042861
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042861'
/scratch/stefan/7769623/working/building/REAL300000042861 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042861

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042861/0 /scratch/stefan/7769623/working/building/REAL300000042861 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/944
`/scratch/stefan/7769623/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(Br)C(F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042861 none CC1=CC=C(Br)C(F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 73, 101, 101, 101, 101, 101, 101, 101, 101, 2, 2, 2, 1, 1, 12, 73, 101, 101, 101, 101] 101
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042861 none CC1=CC=C(Br)C(F)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 100, 101, 101, 101, 101, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 101, 101, 101, 101, 55, 12, 1, 1, 1, 1] 101
rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 159
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042861 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042861
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042861/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042861
Building REAL300000042862
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042862'
/scratch/stefan/7769623/working/building/REAL300000042862 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042862

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042862/0 /scratch/stefan/7769623/working/building/REAL300000042862 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/945
`/scratch/stefan/7769623/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1)

`REAL300000042862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042862 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 48, 48, 113, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 2, 2, 2, 1, 1, 15, 15, 15, 48, 113, 131, 131, 131, 131, 2, 2, 2, 1] 131
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 331
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: REAL300000042862 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [129, 129, 131, 131, 119, 57, 57, 57, 31, 57, 57, 57, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 131, 131, 131, 131, 131, 131, 131, 131, 57, 57, 57, 30, 7, 1, 1, 1, 1, 131, 131, 131, 131] 131
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 345
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042862 none CC1=CC=C(OC2=CC(Cl)=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [7, 6, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 57, 57, 57, 57, 57, 57, 57, 57, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 11, 29, 57, 57, 57, 57, 15, 15, 15, 15] 131
rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 188
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042862 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042862
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042862/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042862
Building REAL300000042863
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042863'
/scratch/stefan/7769623/working/building/REAL300000042863 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042863

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042863/0 /scratch/stefan/7769623/working/building/REAL300000042863 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/946
`/scratch/stefan/7769623/working/3D/946' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042863 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 46, 81, 81, 81, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 2, 2, 2, 8, 46, 81, 81, 81, 81] 81
rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 11, 26, 27] set([6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 179
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042863 none CC1=CC=C([N+](=O)[O-])C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 61, 81, 81, 81, 81, 81, 81, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 81, 81, 81, 81, 65, 81, 81, 81, 40, 12, 1, 1, 1, 1] 81
rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 180
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042863 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042863
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042863/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042863
Building REAL300000042864
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042864'
/scratch/stefan/7769623/working/building/REAL300000042864 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042864

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042864/0 /scratch/stefan/7769623/working/building/REAL300000042864 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/947
`/scratch/stefan/7769623/working/3D/947' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)=C1)

`REAL300000042864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042864 none O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 27, 27, 27, 16, 16, 16, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 16, 16, 1] 27
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 48, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 83
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: REAL300000042864 none O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 27, 27, 27, 24, 24, 11, 11, 11, 11, 11, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 11, 11, 27] 27
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 58
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042864 none O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@H+](CC4=CC=CC=C4)C[C@H]23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 9, 11, 11, 1, 1, 1, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 1, 1, 16] 27
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 48])
total number of confs: 60
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042864 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042864/1 /scratch/stefan/7769623/working/building/REAL300000042864 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/948
`/scratch/stefan/7769623/working/3D/948' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)=C1)

`REAL300000042864.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042864/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042864 none O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 19, 19, 19, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 27, 27, 27, 27, 19, 19, 1] 27
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 48, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 84
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: REAL300000042864 none O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 27, 27, 27, 24, 24, 8, 8, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 8, 8, 27] 27
rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 52
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042864 none O=C([O-])C1=CC=CC(N=NC2CC[C@@H]3C[N@@H+](CC4=CC=CC=C4)C[C@H]23)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 19, 19, 19, 19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 5, 8, 8, 1, 1, 1, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 1, 1, 19] 27
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 48])
total number of confs: 56
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042864 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042864
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042864/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042864/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042864
Building REAL300000042865
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042865'
/scratch/stefan/7769623/working/building/REAL300000042865 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042865

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042865/0 /scratch/stefan/7769623/working/building/REAL300000042865 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/949
`/scratch/stefan/7769623/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C(C)NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042865 none COC(=O)C1=C(C)NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 23, 38, 38, 38, 38, 38, 38, 38, 38, 1, 13, 13, 13, 2, 2, 2, 1, 7, 23, 38, 38, 38, 38, 1] 65
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 21, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042865 none COC(=O)C1=C(C)NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 38, 65, 38, 38, 38, 38, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 65, 65, 65, 38, 38, 38, 38, 24, 8, 1, 1, 1, 1, 38] 65
rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 175
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042865 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042865
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042865/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042865
Building REAL300000042866
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042866'
/scratch/stefan/7769623/working/building/REAL300000042866 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042866

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042866/0 /scratch/stefan/7769623/working/building/REAL300000042866 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/950
`/scratch/stefan/7769623/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(F)C=CC=C1[N+](=O)[O-])

`REAL300000042866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042866 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 41, 41, 41, 39, 41, 41, 41, 42, 42, 33, 33, 33, 9, 1, 1, 1, 1, 41, 41, 41] 42
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33])
total number of confs: 90
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042866 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [4, 1, 4, 4, 22, 41, 41, 41, 41, 41, 42, 42, 41, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 22, 41, 41, 41, 41, 1, 1, 1] 42
rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 96
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042866 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042866
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042866/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042866
Building REAL300000042867
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042867'
/scratch/stefan/7769623/working/building/REAL300000042867 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042867

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042867/0 /scratch/stefan/7769623/working/building/REAL300000042867 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/951
`/scratch/stefan/7769623/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NS(=O)(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042867 none NS(=O)(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 58, 102, 102, 102, 102, 102, 102, 102, 102, 1, 5, 5, 1, 1, 1, 11, 58, 102, 102, 102, 102, 1] 201
rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 21, 24, 25, 26] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 225
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042867 none NS(=O)(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 102, 201, 201, 102, 63, 102, 102, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 102, 201, 201, 63, 102, 102, 63, 12, 1, 1, 1, 1, 102] 201
rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 676
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042867 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042867
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042867/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042867
Building REAL300000042868
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042868'
/scratch/stefan/7769623/working/building/REAL300000042868 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042868

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042868/0 /scratch/stefan/7769623/working/building/REAL300000042868 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/952
`/scratch/stefan/7769623/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN2C=C(CN=NC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1)

`REAL300000042868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042868 none COC1=CC=C(CN2C=C(CN=NC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 60, 180, 180, 201, 201, 201, 201, 201, 201, 201, 201, 22, 22, 1, 1, 2, 2, 2, 1, 1, 6, 6, 22, 60, 60, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 41, 24, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 420
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042868 none COC1=CC=C(CN2C=C(CN=NC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 165, 76, 76, 76, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 76, 76, 201, 201, 201, 201, 201, 201, 201, 165, 165, 76, 34, 34, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 644
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042868 none COC1=CC=C(CN2C=C(CN=NC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 13, 13, 22, 22, 7, 1, 1, 1, 1, 1, 6, 39, 39, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 22, 22, 22, 22, 22, 22, 22, 7, 7, 1, 6, 6, 76, 76, 76, 76, 22, 22] 201
rigid atoms, others: [33, 6, 7, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 198
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042868 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042868/1 /scratch/stefan/7769623/working/building/REAL300000042868 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/953
`/scratch/stefan/7769623/working/3D/953' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(CN2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1)

`REAL300000042868.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042868/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042868 none COC1=CC=C(CN2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 44, 44, 148, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 1, 1, 2, 2, 2, 1, 1, 6, 6, 33, 44, 148, 201, 201, 201, 201, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 41, 24, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 450
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042868 none COC1=CC=C(CN2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 130, 40, 40, 40, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 201, 201, 201, 201, 201, 201, 201, 130, 130, 40, 30, 8, 1, 1, 1, 1, 201, 201] 201
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 548
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042868 none COC1=CC=C(CN2C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)N=N2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 17, 17, 33, 33, 9, 1, 1, 1, 1, 1, 5, 5, 17, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 33, 33, 33, 33, 33, 33, 33, 9, 9, 1, 5, 17, 40, 40, 40, 40, 33, 33] 201
rigid atoms, others: [33, 6, 7, 8, 9, 10, 22, 23] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 200
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042868 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042868
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042868/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042868/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042868
Building REAL300000042869
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042869'
/scratch/stefan/7769623/working/building/REAL300000042869 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042869

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042869/0 /scratch/stefan/7769623/working/building/REAL300000042869 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/954
`/scratch/stefan/7769623/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=NN2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1)

`REAL300000042869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042869 none COC(=O)C1=NN2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 12, 12, 12, 1, 1, 1, 1, 1, 1, 5, 26, 26, 26, 26, 1] 46
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 22, 23, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26])
total number of confs: 60
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042869 none COC(=O)C1=NN2CCCC(=NNC3=CC=CC(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 26, 46, 26, 26, 26, 26, 26, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 46, 46, 46, 26, 26, 26, 26, 26, 26, 10, 1, 1, 1, 1, 26] 46
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 121
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042869 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042869
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042869/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042869
Building REAL300000042870
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042870'
/scratch/stefan/7769623/working/building/REAL300000042870 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042870

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042870/0 /scratch/stefan/7769623/working/building/REAL300000042870 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/955
`/scratch/stefan/7769623/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1)

`REAL300000042870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042870 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 20, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 13, 13, 13, 1, 1, 5, 20, 47, 47, 47, 47, 1] 62
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042870 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 46, 62, 46, 47, 47, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 47, 62, 62, 62, 47, 47, 41, 10, 1, 1, 1, 1, 47] 62
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 138
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042870 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042870
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042870/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042870
Building REAL300000042871
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042871'
/scratch/stefan/7769623/working/building/REAL300000042871 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042871

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042871/0 /scratch/stefan/7769623/working/building/REAL300000042871 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/956
`/scratch/stefan/7769623/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)=C1)

`REAL300000042871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042871 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 51, 51, 51, 51, 51, 151, 201, 201, 201, 201, 201, 51, 1, 1, 1, 1, 7, 23, 51, 51, 51, 201, 201, 201, 201, 51, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042871 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 169, 93, 93, 33, 33, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 33, 201, 201, 201, 201, 169, 93, 33, 33, 33, 1, 1, 1, 1, 33, 201] 201
rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 497
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042871 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=CC=N3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 50, 51, 51, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 33, 33, 33, 33, 33, 1, 51, 50, 51, 51, 24, 6, 1, 1, 1, 33, 33, 33, 33, 1, 51] 201
rigid atoms, others: [32, 37, 10, 11, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042871 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042871
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042871/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042871
Building REAL300000042872
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042872'
/scratch/stefan/7769623/working/building/REAL300000042872 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042872

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042872/0 /scratch/stefan/7769623/working/building/REAL300000042872 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/957
`/scratch/stefan/7769623/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(COC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)=C1)

`REAL300000042872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042872 none COC1=CC=CC(COC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 43, 43, 130, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 43, 129, 201, 201, 201, 201, 9, 9, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 46, 27, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042872 none COC1=CC=CC(COC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 47, 47, 46, 36, 46, 46, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 47, 47, 46, 46, 20, 4, 1, 1, 1, 1, 46, 46, 201] 201
rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46])
total number of confs: 321
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042872 none COC1=CC=CC(COC2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 24, 47, 47, 47, 47, 47, 47, 47, 46, 1, 1, 9, 17, 17, 17, 9, 9, 9, 2, 2, 1, 1, 8, 24, 47, 47, 47, 46, 1, 1, 9] 201
rigid atoms, others: [45, 36, 37, 8, 9, 10, 11, 12, 13, 44, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46])
total number of confs: 117
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042872 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042872
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042872/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042872
Building REAL300000042873
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042873'
/scratch/stefan/7769623/working/building/REAL300000042873 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042873

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042873/0 /scratch/stefan/7769623/working/building/REAL300000042873 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/958
`/scratch/stefan/7769623/working/3D/958' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)=C1)

`REAL300000042873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042873 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 95, 95, 95, 95, 95, 196, 201, 201, 201, 201, 201, 201, 95, 1, 1, 1, 1, 9, 38, 95, 95, 95, 196, 196, 201, 201, 201, 201, 201, 95, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 596
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: REAL300000042873 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 168, 55, 55, 16, 16, 16, 16, 16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 168, 55, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 16, 201] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42])
total number of confs: 495
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042873 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(COC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 94, 95, 95, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 1, 95, 94, 95, 95, 53, 8, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 1, 95] 201
rigid atoms, others: [32, 33, 41, 10, 11, 12, 13, 14, 15, 16, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 42])
total number of confs: 224
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042873 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042873
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042873/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042873
Building REAL300000042874
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042874'
/scratch/stefan/7769623/working/building/REAL300000042874 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042874

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042874/0 /scratch/stefan/7769623/working/building/REAL300000042874 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/959
`/scratch/stefan/7769623/working/3D/959' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC(F)F)=C1)

`REAL300000042874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042874 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 46, 46, 27, 46, 46, 46, 105, 197, 201, 201, 1, 1, 1, 1, 7, 27, 46, 46, 46, 46, 197, 197, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 705
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042874 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OCC(F)F)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 83, 83, 46, 46, 46, 46, 21, 4, 1, 1, 1, 1, 27, 27, 83, 46] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 404
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042874 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042874
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042874/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042874
Building REAL300000042875
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042875'
/scratch/stefan/7769623/working/building/REAL300000042875 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042875

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042875/0 /scratch/stefan/7769623/working/building/REAL300000042875 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/960
`/scratch/stefan/7769623/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC3=C(Br)C=C(F)C=C3N2)=C1)

`REAL300000042875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042875 none O=C([O-])C1=CC=CC(NN=CC2=CC3=C(Br)C=C(F)C=C3N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 13, 37, 44, 44, 44, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 72
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042875 none O=C([O-])C1=CC=CC(NN=CC2=CC3=C(Br)C=C(F)C=C3N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 43, 44, 44, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 43, 44, 44, 25, 6, 1, 1, 1, 1, 44] 44
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042875 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042875
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042875/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042875
Building REAL300000042876
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042876'
/scratch/stefan/7769623/working/building/REAL300000042876 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042876

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042876/0 /scratch/stefan/7769623/working/building/REAL300000042876 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/961
`/scratch/stefan/7769623/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=C(C2=CC=CS2)O1)

`REAL300000042876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042876 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=C(C2=CC=CS2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 14, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 11, 11, 46, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 13, 13, 13, 13, 1, 2, 2, 2, 11, 46, 72, 72, 72, 72, 13, 13, 13] 132
rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
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: REAL300000042876 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=C(C2=CC=CS2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 14, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 63, 63, 110, 132, 132, 132, 132, 132, 132, 132, 132, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 62, 110, 132, 132, 132, 132, 1, 1, 1] 132
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: 310
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042876 none CC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N=C(C2=CC=CS2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 14, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 72, 72, 72, 132, 132, 132, 132, 72, 72, 72, 72, 28, 6, 1, 1, 1, 1, 132, 132, 132] 132
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34])
total number of confs: 217
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042876 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042876
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042876/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042876
Building REAL300000042877
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042877'
/scratch/stefan/7769623/working/building/REAL300000042877 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042877

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042877/0 /scratch/stefan/7769623/working/building/REAL300000042877 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/962
`/scratch/stefan/7769623/working/3D/962' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1)

`REAL300000042877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042877 none COC(=O)C1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 8, 42, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 13, 13, 13, 1, 1, 8, 8, 8, 42, 105, 105, 105, 105, 2, 2, 2, 1] 180
rigid atoms, others: [2, 4, 5, 6, 7, 8, 40, 21, 22, 23, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 225
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042877 none COC(=O)C1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [180, 180, 87, 180, 67, 105, 105, 46, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 105, 105, 105, 180, 180, 180, 105, 105, 46, 46, 46, 12, 1, 1, 1, 1, 105, 105, 105, 105] 180
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40])
total number of confs: 601
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042877 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042877
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042877/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042877
Building REAL300000042878
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042878'
/scratch/stefan/7769623/working/building/REAL300000042878 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042878

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042878/0 /scratch/stefan/7769623/working/building/REAL300000042878 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/963
`/scratch/stefan/7769623/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=C2)=C1)

`REAL300000042878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042878 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 111, 111, 111, 111, 111, 201, 201, 201, 201, 111, 37, 37, 37, 8, 1, 1, 1, 1, 111, 111, 111, 201, 201, 201, 111] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 346
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: REAL300000042878 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 42, 42, 134, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 42, 42, 42, 134, 201, 201, 201, 201, 6, 7, 7, 1, 1, 1, 7] 201
rigid atoms, others: [35, 36, 37, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 455
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042878 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 12, 12, 63, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 12, 12, 12, 63, 111, 111, 111, 111, 1, 1, 1, 7, 6, 7, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37])
total number of confs: 244
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042878 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042878
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042878/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042878
Building REAL300000042879
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042879'
/scratch/stefan/7769623/working/building/REAL300000042879 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042879

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042879/0 /scratch/stefan/7769623/working/building/REAL300000042879 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/964
`/scratch/stefan/7769623/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)=C1)

`REAL300000042879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042879 none O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 31, 138, 164, 168, 168, 164, 168, 168, 31, 97, 97, 97, 97, 97, 1, 1, 1, 1, 9, 138, 138, 164, 164, 168, 168, 164, 168, 168, 97, 97, 97, 97, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 712
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042879 none O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 38, 7, 7, 1, 7, 55, 65, 71, 71, 65, 71, 71, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 38, 55, 55, 65, 65, 71, 71, 65, 71, 71, 1, 1, 1, 1, 97] 201
rigid atoms, others: [39, 40, 41, 10, 19, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43])
total number of confs: 427
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042879 none O=C([O-])C1=CC=CC(NN=C(CCC2=CC=CC=C2)C2=CC=CN=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 168, 168, 168, 168, 168, 168, 84, 22, 22, 7, 4, 1, 1, 1, 1, 1, 1, 1, 22, 71, 71, 71, 71, 71, 168, 168, 168, 168, 84, 7, 7, 4, 4, 1, 1, 1, 1, 1, 71, 71, 71, 71, 168] 201
rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43])
total number of confs: 412
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042879 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042879
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042879/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042879
Building REAL300000042880
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042880'
/scratch/stefan/7769623/working/building/REAL300000042880 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042880

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042880/0 /scratch/stefan/7769623/working/building/REAL300000042880 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/965
`/scratch/stefan/7769623/working/3D/965' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1)

`REAL300000042880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042880 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 106, 106, 106, 106, 106, 106, 106, 189, 201, 201, 189, 189, 201, 201, 33, 33, 33, 9, 1, 1, 1, 1, 106, 106, 106, 201, 201, 201, 201] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042880 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 16, 63, 63, 167, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 167, 201, 201, 201, 201, 16, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 486
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042880 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(F)=CC=C1OC1=CC=C(Cl)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 45, 106, 106, 106, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 8, 8, 16, 16, 9, 9, 9, 45, 106, 106, 106, 106, 1, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [1, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042880 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042880
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042880/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042880
Building REAL300000042881
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042881'
/scratch/stefan/7769623/working/building/REAL300000042881 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042881

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042881/0 /scratch/stefan/7769623/working/building/REAL300000042881 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/966
`/scratch/stefan/7769623/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)S1)

`REAL300000042881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042881 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 68, 68, 68, 68, 69, 69, 69, 68, 43, 43, 43, 10, 1, 1, 1, 1, 68, 68] 69
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 121
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042881 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 1, 12, 12, 42, 69, 69, 69, 69, 69, 69, 69, 68, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 42, 69, 69, 69, 68, 1, 1] 69
rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 166
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042881 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042881
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042881/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042881
Building REAL300000042882
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042882'
/scratch/stefan/7769623/working/building/REAL300000042882 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042882

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042882/0 /scratch/stefan/7769623/working/building/REAL300000042882 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/967
`/scratch/stefan/7769623/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])[N-]1)

`REAL300000042882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042882 none COC(=O)C1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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: [10, 10, 1, 10, 1, 1, 1, 1, 8, 8, 8, 28, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 2, 2, 1, 11, 10, 10, 1, 8, 8, 8, 28, 44, 44, 44, 44] 64
rigid atoms, others: [2, 4, 5, 6, 7, 20, 21, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042882 none COC(=O)C1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 44, 64, 44, 44, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 44, 44, 64, 64, 64, 44, 23, 23, 23, 7, 1, 1, 1, 1] 64
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 145
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042882 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042882/1 /scratch/stefan/7769623/working/building/REAL300000042882 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/968
`/scratch/stefan/7769623/working/3D/968' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])[N-]1)

`REAL300000042882.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042882/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042882 none COC(=O)C1=CC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [8, 8, 1, 8, 1, 1, 1, 1, 5, 5, 25, 25, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 8, 8, 8, 1, 5, 5, 5, 5, 41, 41, 41, 41] 53
rigid atoms, others: [2, 4, 5, 6, 7, 20, 21, 22, 23, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042882 none COC(=O)C1=CC(C(C)N=NC2=CC=CC(C(=O)[O-])=C2)=C([N+](=O)[O-])[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [53, 53, 41, 53, 41, 41, 22, 8, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 53, 53, 53, 41, 22, 22, 22, 22, 1, 1, 1, 1] 53
rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042882 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042882
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042882/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042882/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042882
Building REAL300000042883
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042883'
/scratch/stefan/7769623/working/building/REAL300000042883 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042883

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042883/0 /scratch/stefan/7769623/working/building/REAL300000042883 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/969
`/scratch/stefan/7769623/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(Br)N=C3COCCN32)=C1)

`REAL300000042883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042883 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)N=C3COCCN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 12, 36, 42, 42, 42, 42, 42, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042883 none O=C([O-])C1=CC=CC(NN=CC2=C(Br)N=C3COCCN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 8, 1, 5, 12, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 42, 42, 42, 42, 29, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 29, 9, 1, 1, 1, 1, 1, 1, 42] 42
rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 21, 22, 23, 24, 25, 26])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042883 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042883
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042883/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042883
Building REAL300000042884
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042884'
/scratch/stefan/7769623/working/building/REAL300000042884 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042884

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042884/0 /scratch/stefan/7769623/working/building/REAL300000042884 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/970
`/scratch/stefan/7769623/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)OC)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1)

`REAL300000042884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042884 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', '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, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 11, 11, 11, 1, 1, 1, 8, 8, 34, 63, 63, 63, 63, 63, 64, 64, 63, 1, 6, 6, 6, 6, 6, 11, 11, 11, 1, 8, 34, 63, 63, 63, 63, 1] 159
rigid atoms, others: [1, 2, 3, 4, 38, 8, 9, 10, 22, 31] set([0, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042884 none CCC1=C(C(=O)OC)C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', '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, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [109, 63, 63, 63, 63, 121, 121, 121, 63, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 63, 109, 109, 109, 109, 109, 121, 121, 121, 63, 36, 8, 1, 1, 1, 1, 63] 159
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 536
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042884 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042884
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042884/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042884
Building REAL300000042885
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042885'
/scratch/stefan/7769623/working/building/REAL300000042885 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042885

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042885/0 /scratch/stefan/7769623/working/building/REAL300000042885 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/971
`/scratch/stefan/7769623/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1)

`REAL300000042885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042885 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 83, 83, 83, 122, 122, 197, 201, 201, 201, 83, 68, 68, 68, 68, 68, 43, 1, 1, 1, 1, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 83] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 764
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042885 none CCC(N=NC1=CC=CC(C(=O)[O-])=C1)C1CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 8, 1, 11, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 6, 32, 32, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 5, 5, 10, 12, 12, 12, 1, 9, 9, 9, 9, 9, 6, 83, 83, 83, 83, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [48, 2, 35, 36, 37, 14, 15, 16, 17, 24, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 172
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042885 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042885
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042885/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042885
Building REAL300000042886
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042886'
/scratch/stefan/7769623/working/building/REAL300000042886 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042886

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042886/0 /scratch/stefan/7769623/working/building/REAL300000042886 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/972
`/scratch/stefan/7769623/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CN=C2)=N1)

`REAL300000042886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042886 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CN=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 39, 39, 8, 39, 1, 1, 1, 1, 1, 3, 3, 10, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 5, 5, 5, 5, 5, 1, 63, 63, 63, 63, 63, 8, 8, 1, 3, 10, 15, 15, 15, 15, 5, 5, 5, 5] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 21, 22, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042886 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CN=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 113, 113, 27, 113, 5, 5, 5, 5, 5, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 5, 129, 129, 129, 129, 129, 27, 27, 5, 6, 20, 27, 27, 27, 27, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 458
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042886 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CC=CN=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [128, 99, 99, 32, 99, 15, 15, 15, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 27, 27, 27, 27, 27, 15, 128, 128, 128, 128, 128, 32, 32, 15, 14, 4, 1, 1, 1, 1, 27, 27, 27, 27] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46])
total number of confs: 467
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042886 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042886
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042886/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042886
Building REAL300000042887
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042887'
/scratch/stefan/7769623/working/building/REAL300000042887 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042887

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042887/0 /scratch/stefan/7769623/working/building/REAL300000042887 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/973
`/scratch/stefan/7769623/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=N1)

`REAL300000042887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042887 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 37, 37, 6, 37, 1, 1, 1, 1, 1, 4, 4, 15, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 9, 9, 9, 9, 9, 1, 57, 57, 57, 57, 57, 6, 6, 1, 4, 15, 19, 19, 19, 19, 9, 9, 9, 9, 9] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 21, 22, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042887 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 122, 122, 28, 122, 9, 9, 9, 9, 9, 10, 10, 27, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 9, 154, 154, 154, 154, 154, 28, 28, 9, 10, 27, 31, 31, 31, 31, 1, 2, 2, 2, 1] 201
rigid atoms, others: [43, 47, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 576
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042887 none CCOC(=O)CN1C=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(C2=CN(C)N=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 135, 135, 39, 135, 19, 19, 19, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 31, 31, 31, 31, 31, 19, 152, 152, 152, 152, 152, 39, 39, 19, 15, 6, 1, 1, 1, 1, 31, 31, 31, 31, 31] 201
rigid atoms, others: [39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47])
total number of confs: 509
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042887 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042887
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042887/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042887
Building REAL300000042888
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042888'
/scratch/stefan/7769623/working/building/REAL300000042888 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042888

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042888/0 /scratch/stefan/7769623/working/building/REAL300000042888 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/974
`/scratch/stefan/7769623/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042888 none CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 41, 6, 1, 1, 1, 1, 1, 5, 5, 11, 13, 13, 13, 1, 17, 50, 50, 94, 94, 94, 94, 94, 94, 94, 94, 41, 41, 41, 41, 41, 41, 41, 17, 6, 6, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 94, 94, 94, 94] 201
rigid atoms, others: [4, 37, 6, 7, 8, 39, 15, 49, 50, 38, 5] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042888 none CC(C)C(CC1CN(C(=O)OC(C)(C)C)C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 25, 53, 7, 25, 52, 94, 94, 94, 124, 124, 176, 179, 179, 179, 94, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 25, 54, 54, 94, 94, 94, 179, 179, 179, 179, 179, 179, 179, 179, 179, 94, 94, 1, 1, 1, 1] 201
rigid atoms, others: [51, 54, 17, 18, 19, 20, 21, 22, 23, 52, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 709
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042888 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042888
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042888/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042888
Building REAL300000042889
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042889'
/scratch/stefan/7769623/working/building/REAL300000042889 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042889

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042889/0 /scratch/stefan/7769623/working/building/REAL300000042889 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/975
`/scratch/stefan/7769623/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)=C1)

`REAL300000042889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042889 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 32, 32, 73, 73, 73, 38, 73, 73, 73, 140, 201, 201, 201, 140, 201, 201, 201, 1, 1, 1, 1, 9, 32, 73, 37, 73, 201, 144, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 27, 28, 29, 30] set([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: 591
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042889 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 171, 75, 75, 21, 21, 21, 18, 20, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 171, 75, 21, 21, 21, 1, 1, 1, 201] 201
rigid atoms, others: [36, 37, 38, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39])
total number of confs: 474
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042889 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC(F)=CC(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 72, 73, 73, 44, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 8, 18, 18, 18, 73, 72, 73, 73, 44, 12, 1, 1, 1, 18, 8, 18, 73] 201
rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042889 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042889
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042889/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042889
Building REAL300000042890
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042890'
/scratch/stefan/7769623/working/building/REAL300000042890 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042890

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042890/0 /scratch/stefan/7769623/working/building/REAL300000042890 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/976
`/scratch/stefan/7769623/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042890 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 21, 21, 53, 53, 141, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 4, 1, 2, 2, 2, 1, 1, 21, 21, 21, 21, 53, 141, 201, 201, 201, 201] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 36, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 472
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042890 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 184, 201, 201, 201, 128, 55, 55, 55, 28, 55, 55, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 55, 55, 55, 27, 9, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 503
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042890 none COC1=CC(C)=CC=C1OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 21, 21, 21, 15, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 55, 55, 55, 55, 55, 55, 55, 55, 39, 39, 39, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 10, 29, 55, 55, 55, 55] 201
rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46])
total number of confs: 194
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042890 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042890
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042890/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042890
Building REAL300000042891
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042891'
/scratch/stefan/7769623/working/building/REAL300000042891 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042891

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042891/0 /scratch/stefan/7769623/working/building/REAL300000042891 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/977
`/scratch/stefan/7769623/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)=C1)

`REAL300000042891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042891 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 87, 87, 87, 84, 87, 87, 87, 191, 201, 201, 191, 191, 201, 201, 1, 1, 1, 1, 10, 45, 87, 87, 87, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 26, 27, 28, 29] set([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: 349
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042891 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 162, 57, 57, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 162, 57, 16, 16, 16, 1, 1, 1, 1, 201] 201
rigid atoms, others: [35, 36, 37, 38, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 470
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042891 none O=C([O-])C1=CC=CC(NN=CC2=CC(F)=CC=C2OC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 38, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 8, 8, 16, 16, 87, 87, 87, 87, 38, 12, 1, 1, 1, 16, 16, 16, 16, 87] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39])
total number of confs: 192
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042891 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042891
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042891/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042891
Building REAL300000042892
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042892'
/scratch/stefan/7769623/working/building/REAL300000042892 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042892

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042892/0 /scratch/stefan/7769623/working/building/REAL300000042892 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/978
`/scratch/stefan/7769623/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CN=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042892 none COC(=O)C1=CN=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 67, 136, 136, 136, 136, 136, 136, 136, 136, 1, 12, 12, 12, 1, 1, 13, 13, 13, 67, 136, 136, 136, 136, 1] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 22, 36, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 292
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042892 none COC(=O)C1=CN=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 136, 201, 136, 136, 136, 136, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 136, 201, 201, 201, 136, 136, 36, 36, 36, 8, 1, 1, 1, 1, 136] 201
rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 431
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042892 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042892
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042892/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042892
Building REAL300000042893
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042893'
/scratch/stefan/7769623/working/building/REAL300000042893 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042893

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042893/0 /scratch/stefan/7769623/working/building/REAL300000042893 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/979
`/scratch/stefan/7769623/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042893 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 63, 63, 138, 166, 166, 166, 166, 166, 166, 166, 166, 1, 1, 7, 7, 7, 1, 1, 28, 28, 28, 63, 138, 166, 166, 166, 166, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 42, 43, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042893 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 153, 121, 166, 166, 121, 54, 54, 54, 24, 54, 54, 54, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 166, 166, 201, 201, 201, 166, 166, 54, 24, 54, 23, 5, 1, 1, 1, 1, 166, 166] 201
rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43])
total number of confs: 594
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042893 none CSC1=CC=C(OC2=CC=C(F)C=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 8, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 54, 54, 54, 54, 54, 54, 54, 54, 28, 28, 66, 66, 66, 28, 28, 1, 1, 1, 10, 27, 54, 54, 54, 54, 28, 28] 201
rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 247
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042893 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042893
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042893/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042893
Building REAL300000042894
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042894'
/scratch/stefan/7769623/working/building/REAL300000042894 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042894

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042894/0 /scratch/stefan/7769623/working/building/REAL300000042894 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/980
`/scratch/stefan/7769623/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CNC(Br)=C2)=C1)

`REAL300000042894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042894 none O=C([O-])C1=CC=CC(NN=CC2=CNC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 40, 40, 61, 61, 61, 61, 61, 1, 1, 1, 1, 12, 40, 61, 61, 61, 1] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25])
total number of confs: 102
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042894 none O=C([O-])C1=CC=CC(NN=CC2=CNC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'Br', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 45, 9, 9, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 45, 9, 1, 1, 1, 61] 61
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 26])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042894 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042894
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042894/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042894
Building REAL300000042895
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042895'
/scratch/stefan/7769623/working/building/REAL300000042895 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042895

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042895/0 /scratch/stefan/7769623/working/building/REAL300000042895 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/981
`/scratch/stefan/7769623/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1OC)

`REAL300000042895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042895 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 25, 54, 54, 53, 54, 54, 54, 54, 54, 1, 1, 1, 1, 6, 4, 4, 4, 1, 1, 7, 25, 54, 54, 53, 54, 7, 7, 7] 79
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042895 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(F)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 54, 54, 54, 54, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 54, 54, 54, 79, 79, 79, 79, 54, 54, 32, 9, 1, 1, 1, 1, 79, 79, 79] 79
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 185
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042895 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042895
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042895/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042895
Building REAL300000042896
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042896'
/scratch/stefan/7769623/working/building/REAL300000042896 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042896

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042896/0 /scratch/stefan/7769623/working/building/REAL300000042896 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/982
`/scratch/stefan/7769623/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042896 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 1, 1, 1, 12, 12, 51, 71, 71, 71, 71, 71, 71, 71, 70, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 2, 2, 2, 12, 51, 71, 71, 71, 70] 99
rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 181
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042896 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [71, 70, 70, 70, 70, 99, 99, 99, 99, 99, 99, 70, 70, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 71, 71, 99, 99, 99, 99, 99, 99, 99, 71, 71, 71, 28, 6, 1, 1, 1, 1] 99
rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 169
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042896 none CC1=NN(C2=CC=CC=C2C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 33, 81, 99, 99, 99, 99, 99, 99, 99, 99, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 33, 81, 99, 99, 99, 99] 99
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 246
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042896 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042896
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042896/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042896
Building REAL300000042897
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042897'
/scratch/stefan/7769623/working/building/REAL300000042897 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042897

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042897/0 /scratch/stefan/7769623/working/building/REAL300000042897 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/983
`/scratch/stefan/7769623/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1SC(F)(F)F)

`REAL300000042897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042897 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1SC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 120, 120, 120, 120, 120, 120, 201, 201, 201, 201, 37, 37, 37, 8, 1, 1, 1, 1, 120, 120, 120, 120] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 318
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042897 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC=C1SC(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 39, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 7, 7, 7, 39, 120, 120, 120, 120, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 255
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042897 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042897
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042897/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042897
Building REAL300000042898
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042898'
/scratch/stefan/7769623/working/building/REAL300000042898 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042898

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042898/0 /scratch/stefan/7769623/working/building/REAL300000042898 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/984
`/scratch/stefan/7769623/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC2=CC=CC=C12)

`REAL300000042898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042898 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 87, 87, 87, 87, 87, 87, 87, 87, 40, 40, 40, 8, 1, 1, 1, 1, 87, 87, 87, 87, 87] 87
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34])
total number of confs: 141
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042898 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC2=CC=CC=C12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [10, 1, 10, 10, 54, 87, 87, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 54, 87, 87, 87, 87, 1, 1, 1, 1, 1] 87
rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 183
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042898 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042898
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042898/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042898
Building REAL300000042899
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042899'
/scratch/stefan/7769623/working/building/REAL300000042899 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042899

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042899/0 /scratch/stefan/7769623/working/building/REAL300000042899 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/985
`/scratch/stefan/7769623/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)C2=C1)

`REAL300000042899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042899 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 5, 12, 17, 17, 17, 17, 1] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 22, 23, 24, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042899 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 17] 17
rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 29
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042899 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042899
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042899/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042899
Building REAL300000042900
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042900'
/scratch/stefan/7769623/working/building/REAL300000042900 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042900

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042900/0 /scratch/stefan/7769623/working/building/REAL300000042900 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/986
`/scratch/stefan/7769623/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(Cl)=C1OC(C)C(=O)[O-])

`REAL300000042900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042900 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 6, 6, 30, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 7, 16, 16, 23, 23, 4, 4, 4, 1, 6, 30, 62, 62, 62, 61, 1, 16, 16, 16, 16] 174
rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 206
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042900 none COC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [109, 62, 61, 61, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 61, 61, 61, 61, 136, 166, 166, 174, 174, 109, 109, 109, 61, 21, 5, 1, 1, 1, 1, 61, 166, 166, 166, 166] 174
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41])
total number of confs: 481
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042900 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042900
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042900/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042900
Building REAL300000042901
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042901'
/scratch/stefan/7769623/working/building/REAL300000042901 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042901

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042901/0 /scratch/stefan/7769623/working/building/REAL300000042901 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/987
`/scratch/stefan/7769623/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1)

`REAL300000042901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042901 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 6, 22, 38, 38, 76, 38, 1] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 140
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042901 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [38, 38, 38, 38, 38, 38, 38, 37, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 38, 38, 38, 38, 37, 6, 1, 1, 2, 1, 38] 76
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 29, 31])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042901 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042901
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042901/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042901
Building REAL300000042902
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042902'
/scratch/stefan/7769623/working/building/REAL300000042902 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042902

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042902/0 /scratch/stefan/7769623/working/building/REAL300000042902 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/988
`/scratch/stefan/7769623/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C)

`REAL300000042902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042902 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 9, 9, 53, 114, 114, 114, 114, 114, 114, 114, 114, 1, 1, 1, 11, 11, 11, 1, 1, 9, 52, 114, 114, 114, 113, 1, 2, 2, 2] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 34, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 35, 36, 37])
total number of confs: 234
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042902 none COC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 88, 113, 113, 47, 47, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 113, 113, 114, 201, 201, 201, 113, 113, 47, 8, 1, 1, 1, 1, 114, 114, 114, 114] 201
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 577
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042902 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042902
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042902/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042902
Building REAL300000042903
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042903'
/scratch/stefan/7769623/working/building/REAL300000042903 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042903

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042903/0 /scratch/stefan/7769623/working/building/REAL300000042903 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/989
`/scratch/stefan/7769623/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC(C(=O)[O-])=CC=C2)=C1)

`REAL300000042903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042903 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC(C(=O)[O-])=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 41, 50, 50, 50, 50, 50, 50, 50, 50, 1, 9, 41, 50, 50, 50, 50, 1] 50
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042903 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC(C(=O)[O-])=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 25, 6, 1, 1, 1, 1, 50] 50
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042903 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042903
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042903/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042903
Building REAL300000042904
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042904'
/scratch/stefan/7769623/working/building/REAL300000042904 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042904

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042904/0 /scratch/stefan/7769623/working/building/REAL300000042904 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/990
`/scratch/stefan/7769623/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(F)(F)F)=C1)

`REAL300000042904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042904 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 99, 99, 99, 99, 99, 99, 99, 99, 51, 51, 51, 10, 1, 1, 1, 1, 99, 99] 99
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31])
total number of confs: 165
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042904 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 1, 11, 11, 51, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 51, 99, 99, 99, 99, 1, 1] 99
rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 212
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042904 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042904
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042904/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042904
Building REAL300000042905
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042905'
/scratch/stefan/7769623/working/building/REAL300000042905 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042905

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042905/0 /scratch/stefan/7769623/working/building/REAL300000042905 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/991
`/scratch/stefan/7769623/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSC1=CC=CC=C1CC(C)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042905 none CCSC1=CC=CC=C1CC(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 56, 56, 125, 125, 125, 125, 125, 125, 125, 125, 27, 27, 27, 27, 27, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 125, 125, 125, 125] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 292
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042905 none CCSC1=CC=CC=C1CC(C)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 125, 125, 125, 113, 125, 125, 78, 40, 8, 40, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 125, 125, 125, 125, 78, 78, 40, 40, 40, 40, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 638
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042905 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042905
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042905/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042905
Building REAL300000042906
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042906'
/scratch/stefan/7769623/working/building/REAL300000042906 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042906

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042906/0 /scratch/stefan/7769623/working/building/REAL300000042906 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/992
`/scratch/stefan/7769623/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CN2C(C)(C1)C(N=NC1=CC=CC(C(=O)[O-])=C1)CS2(=O)=O)

`REAL300000042906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 4 of molecule 'REAL300000042906'
Warning: REAL300000042906 failed due to unspecified stereochemistry with strict stereo enabled
Warning: OE3DToAtomStereo is unable to perceive atom stereo from a flat geometry on atom 4 of molecule 'REAL300000042906'
Warning: REAL300000042906 failed due to unspecified stereochemistry with strict stereo enabled
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
Conformer generation failed
Skipping REAL300000042906 0
/scratch/stefan/7769623/working/building/REAL300000042906 /scratch/stefan/7769623/working /scratch/stefan/7769623
`0' -> `0.failed'

Finished preparing REAL300000042906
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Found failed protomers
Marking REAL300000042906 as failed
`/scratch/stefan/7769623/working/building/REAL300000042906' -> `/scratch/stefan/7769623/failed/REAL300000042906'
Building REAL300000042907
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042907'
/scratch/stefan/7769623/working/building/REAL300000042907 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042907

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042907/0 /scratch/stefan/7769623/working/building/REAL300000042907 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/993
`/scratch/stefan/7769623/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(F)C=C3F)C2)=C1)

`REAL300000042907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042907 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(F)C=C3F)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 48, 48, 48, 96, 96, 96, 96, 96, 96, 96, 48, 1, 1, 1, 1, 48, 48, 48, 48, 96, 96, 96, 48, 48, 1] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 175
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: REAL300000042907 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(F)C=C3F)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 70, 70, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 96, 96, 96, 96, 10, 10, 10, 10, 1, 1, 1, 10, 10, 96] 96
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35])
total number of confs: 136
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042907 none O=C([O-])C1=CC=CC(N=NC2CC(C3=CC=C(F)C=C3F)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [48, 48, 48, 48, 48, 48, 48, 13, 13, 1, 1, 1, 1, 1, 10, 10, 3, 9, 10, 10, 10, 1, 48, 48, 48, 48, 1, 1, 1, 1, 10, 10, 10, 1, 1, 48] 96
rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31, 32, 35])
total number of confs: 90
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042907 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042907
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042907/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042907
Building REAL300000042908
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042908'
/scratch/stefan/7769623/working/building/REAL300000042908 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042908

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042908/0 /scratch/stefan/7769623/working/building/REAL300000042908 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/994
`/scratch/stefan/7769623/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1COC2=CC=CC=C2C1)

`REAL300000042908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042908 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 2, 2, 7, 7, 7, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 69, 69, 69, 69, 69, 69, 69, 69, 69, 39, 39, 39, 39, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69] 69
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 232
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042908 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1COC2=CC=CC=C2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 2, 2, 7, 7, 7, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 45, 45, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1] 69
rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 117
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042908 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042908
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042908/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042908
Building REAL300000042909
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042909'
/scratch/stefan/7769623/working/building/REAL300000042909 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042909

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042909/0 /scratch/stefan/7769623/working/building/REAL300000042909 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/995
`/scratch/stefan/7769623/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)SC(CN=NC2=CC=CC(C(=O)[O-])=C2)=N1)

`REAL300000042909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042909 none CC1=C(Br)SC(CN=NC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 62, 62, 108, 108, 108, 108, 108, 108, 108, 108, 1, 2, 2, 2, 9, 9, 108, 108, 108, 108] 108
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 169
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042909 none CC1=C(Br)SC(CN=NC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 108, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 108, 108, 108, 108, 41, 41, 1, 1, 1, 1] 108
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23])
total number of confs: 237
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042909 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042909/1 /scratch/stefan/7769623/working/building/REAL300000042909 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/996
`/scratch/stefan/7769623/working/3D/996' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Br)SC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1)

`REAL300000042909.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042909/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042909 none CC1=C(Br)SC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 44, 44, 44, 44, 44, 44, 44, 44, 1, 2, 2, 2, 7, 35, 44, 44, 44, 44] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 106
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042909 none CC1=C(Br)SC(C=NNC2=CC=CC(C(=O)[O-])=C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 17, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 44, 33, 10, 1, 1, 1, 1] 44
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042909 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042909
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042909/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042909/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042909
Building REAL300000042910
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042910'
/scratch/stefan/7769623/working/building/REAL300000042910 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042910

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042910/0 /scratch/stefan/7769623/working/building/REAL300000042910 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/997
`/scratch/stefan/7769623/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C=C1Cl)

`REAL300000042910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042910 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 60, 60, 40, 60, 60, 60, 60, 41, 41, 41, 11, 1, 1, 1, 1, 60, 60, 120, 60] 120
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 312
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042910 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(O)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 41, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 60, 60, 60, 60, 1, 1, 2, 1] 120
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 132
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042910 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042910
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042910/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042910
Building REAL300000042911
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042911'
/scratch/stefan/7769623/working/building/REAL300000042911 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042911

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042911/0 /scratch/stefan/7769623/working/building/REAL300000042911 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/998
`/scratch/stefan/7769623/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)=N1)

`REAL300000042911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042911 none CN1C=CC(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 69, 75, 75, 75, 75, 75, 75, 75, 75, 10, 10, 1, 2, 2, 2, 1, 1, 30, 69, 75, 75, 75, 75, 10] 75
rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 195
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042911 none CN1C=CC(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 48, 48, 48, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 48, 75, 75, 75, 75, 75, 75, 27, 6, 1, 1, 1, 1, 48] 75
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 122
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042911 none CN1C=CC(C2=NC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CS2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 10, 10, 1, 1, 1, 1, 1, 6, 6, 29, 48, 48, 48, 48, 48, 49, 49, 48, 1, 1, 10, 11, 11, 11, 10, 10, 6, 29, 48, 48, 48, 48, 1] 75
rigid atoms, others: [34, 4, 5, 6, 7, 8, 20, 21] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 116
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042911 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042911
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042911/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042911
Building REAL300000042912
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042912'
/scratch/stefan/7769623/working/building/REAL300000042912 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042912

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042912/0 /scratch/stefan/7769623/working/building/REAL300000042912 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/999
`/scratch/stefan/7769623/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CC=C21)

`REAL300000042912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042912 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 12, 12, 80, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 80, 201, 201, 201, 201, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 364
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042912 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC2=CC=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 60, 60, 60, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 10, 1, 1, 1, 1, 201, 201, 201, 201, 201] 201
rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41])
total number of confs: 276
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042912 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042912
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042912/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042912
Building REAL300000042913
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042913'
/scratch/stefan/7769623/working/building/REAL300000042913 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042913

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042913/0 /scratch/stefan/7769623/working/building/REAL300000042913 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1000
`/scratch/stefan/7769623/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br)

`REAL300000042913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042913 none CC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 10, 10, 28, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 2, 2, 2, 1, 1, 1, 10, 28, 37, 37, 37, 37] 37
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30, 31])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042913 none CC1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 28, 37, 37, 28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 37, 35, 37, 37, 28, 10, 1, 1, 1, 1] 37
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042913 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042913
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042913/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042913
Building REAL300000042914
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042914'
/scratch/stefan/7769623/working/building/REAL300000042914 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042914

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042914/0 /scratch/stefan/7769623/working/building/REAL300000042914 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1001
`/scratch/stefan/7769623/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=C1)

`REAL300000042914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042914 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 53, 53, 53, 53, 53, 168, 201, 201, 201, 201, 201, 201, 53, 1, 1, 1, 1, 5, 21, 53, 53, 53, 201, 201, 201, 201, 53, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 292
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042914 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 162, 79, 79, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 162, 79, 19, 19, 19, 1, 1, 1, 1, 19, 201] 201
rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 502
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042914 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC(OC3=CC=C(F)C=C3)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 53, 53, 53, 53, 27, 7, 1, 1, 1, 19, 19, 19, 19, 1, 53] 201
rigid atoms, others: [32, 33, 38, 10, 11, 12, 13, 14, 15, 16, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 39])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042914 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042914
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042914/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042914
Building REAL300000042915
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042915'
/scratch/stefan/7769623/working/building/REAL300000042915 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042915

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042915/0 /scratch/stefan/7769623/working/building/REAL300000042915 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1002
`/scratch/stefan/7769623/working/3D/1002' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042915 none CN(C)C(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 1, 11, 1, 1, 1, 1, 1, 1, 10, 10, 56, 123, 123, 123, 123, 123, 123, 123, 123, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 10, 56, 123, 123, 123, 123, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22, 38, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37])
total number of confs: 249
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042915 none CN(C)C(=O)C1=CC=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 123, 201, 123, 122, 123, 123, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 123, 201, 201, 201, 201, 201, 201, 122, 123, 123, 38, 8, 1, 1, 1, 1, 123] 201
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 441
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042915 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042915
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042915/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042915
Building REAL300000042916
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042916'
/scratch/stefan/7769623/working/building/REAL300000042916 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042916

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042916/0 /scratch/stefan/7769623/working/building/REAL300000042916 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1003
`/scratch/stefan/7769623/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1CC1CCC1)

`REAL300000042916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042916 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 105, 105, 105, 105, 105, 170, 201, 201, 201, 38, 38, 38, 7, 1, 1, 1, 1, 105, 105, 170, 170, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 639
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042916 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 70, 70, 163, 201, 201, 201, 201, 201, 201, 201, 201, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 70, 70, 70, 163, 201, 201, 201, 201, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 507
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042916 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=NN1CC1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 47, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 10, 10, 10, 47, 105, 105, 105, 105, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 247
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042916 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042916
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042916/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042916
Building REAL300000042917
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042917'
/scratch/stefan/7769623/working/building/REAL300000042917 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042917

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042917/0 /scratch/stefan/7769623/working/building/REAL300000042917 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1004
`/scratch/stefan/7769623/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1)

`REAL300000042917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042917 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
224  conformations in input
total number of sets (complete confs): 224
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 34, 72, 72, 72, 72, 112, 112, 112, 112, 112, 112, 112, 112, 112, 72, 1, 1, 1, 1, 7, 34, 72, 72, 112, 112, 224, 112, 1] 224
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([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: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042917 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
224  conformations in input
total number of sets (complete confs): 224
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 112, 112, 112, 112, 112, 96, 36, 36, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 112, 112, 112, 112, 96, 36, 12, 12, 1, 1, 2, 1, 112] 224
rigid atoms, others: [34, 35, 37, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 38])
total number of confs: 275
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042917 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
224  conformations in input
total number of sets (complete confs): 224
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 39, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 72, 72, 72, 72, 38, 6, 1, 1, 12, 12, 24, 12, 72] 224
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042917 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042917/1 /scratch/stefan/7769623/working/building/REAL300000042917 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1005
`/scratch/stefan/7769623/working/3D/1005' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1)

`REAL300000042917.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042917/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042917 none O=C([O-])C1=CC=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 36, 95, 95, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 1, 1, 1, 1, 36, 35, 95, 95, 201, 201, 402, 201, 1] 402
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([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: 745
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042917 none O=C([O-])C1=CC=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 185, 185, 68, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 68, 68, 12, 12, 1, 1, 2, 1, 201] 402
rigid atoms, others: [34, 35, 37, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 38])
total number of confs: 424
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042917 none O=C([O-])C1=CC=CC(N=NCC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 58, 58, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 95, 95, 95, 95, 9, 9, 1, 1, 12, 12, 24, 12, 95] 402
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042917 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042917
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042917/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042917/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042917
Building REAL300000042918
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042918'
/scratch/stefan/7769623/working/building/REAL300000042918 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042918

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042918/0 /scratch/stefan/7769623/working/building/REAL300000042918 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1006
`/scratch/stefan/7769623/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1S(N)(=O)=O)

`REAL300000042918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042918 none CN1N=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1S(N)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 16, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 2, 2, 2, 1, 8, 16, 21, 21, 21, 21, 4, 4] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042918 none CN1N=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1S(N)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 6, 6, 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: [21, 21, 21, 21, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 25, 25, 25, 21, 21, 21, 21, 12, 6, 1, 1, 1, 1, 25, 25] 25
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 64
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042918 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042918
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042918/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042918
Building REAL300000042919
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042919'
/scratch/stefan/7769623/working/building/REAL300000042919 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042919

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042919/0 /scratch/stefan/7769623/working/building/REAL300000042919 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1007
`/scratch/stefan/7769623/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)NN=C2Cl)=C1)

`REAL300000042919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042919 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)NN=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 12, 47, 47, 115, 115, 154, 154, 115, 115, 115, 115, 1, 1, 1, 1, 12, 47, 154, 154, 154, 154, 154, 115, 1] 154
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 321
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042919 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)NN=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 154, 154, 130, 47, 47, 9, 8, 1, 1, 1, 1, 8, 8, 8, 9, 154, 154, 154, 154, 130, 47, 1, 1, 1, 1, 1, 9, 154] 154
rigid atoms, others: [12, 13, 14, 15, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32])
total number of confs: 365
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042919 none O=C([O-])C1=CC=CC(NN=CC2=C(C3CC3)NN=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 5, 5, 8, 8, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 115, 115, 115, 115, 68, 12, 12, 1, 1, 1, 1, 9, 9, 1, 1, 1, 1, 115, 115, 115, 115, 67, 12, 8, 9, 9, 9, 9, 1, 115] 154
rigid atoms, others: [10, 11, 12, 13, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32])
total number of confs: 251
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042919 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042919
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042919/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042919
Building REAL300000042920
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042920'
/scratch/stefan/7769623/working/building/REAL300000042920 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042920

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042920/0 /scratch/stefan/7769623/working/building/REAL300000042920 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1008
`/scratch/stefan/7769623/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)=C1)

`REAL300000042920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042920 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 73, 73, 167, 167, 175, 175, 167, 167, 175, 175, 167, 167, 167, 167, 167, 167, 167, 167, 1, 1, 1, 1, 13, 73, 175, 175, 175, 175, 167, 167, 167, 1] 175
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 277
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: REAL300000042920 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 123, 33, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 175, 175, 175, 175, 123, 33, 1, 1, 1, 1, 6, 6, 6, 175] 175
rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41])
total number of confs: 384
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042920 none O=C([O-])C1=CC=CC(NN=CC2=C(C3=CC=C(F)C=C3)N=C3C=CC(F)=CN32)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 73, 13, 13, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 73, 13, 6, 6, 6, 6, 1, 1, 1, 167] 175
rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41])
total number of confs: 319
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042920 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042920
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042920/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042920
Building REAL300000042921
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042921'
/scratch/stefan/7769623/working/building/REAL300000042921 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042921

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042921/0 /scratch/stefan/7769623/working/building/REAL300000042921 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1009
`/scratch/stefan/7769623/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC2CCC2)N=C1)

`REAL300000042921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042921 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 87, 87, 87, 162, 201, 201, 201, 87, 87, 24, 24, 24, 4, 1, 1, 1, 1, 87, 162, 162, 201, 201, 201, 201, 201, 201, 201, 87] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 669
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: REAL300000042921 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 24, 93, 93, 194, 201, 201, 201, 201, 201, 201, 201, 201, 24, 24, 6, 1, 1, 1, 1, 1, 24, 24, 93, 93, 93, 194, 201, 201, 201, 201, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 24] 201
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 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, 32, 33, 41])
total number of confs: 532
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042921 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CN(CC2CCC2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 42, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 1, 8, 24, 24, 24, 1, 1, 11, 11, 11, 42, 88, 88, 88, 87, 1, 8, 8, 24, 24, 24, 24, 24, 24, 24, 1] 201
rigid atoms, others: [1, 41, 13, 14, 15, 16, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 250
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042921 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042921
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042921/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042921
Building REAL300000042922
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042922'
/scratch/stefan/7769623/working/building/REAL300000042922 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042922

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042922/0 /scratch/stefan/7769623/working/building/REAL300000042922 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1010
`/scratch/stefan/7769623/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1)

`REAL300000042922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042922 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 12, 12, 12, 74, 197, 197, 197, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 13, 13, 13, 74, 197, 197, 197, 197, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 36, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 362
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042922 none COC1=CC(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 197, 197, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 197, 197, 197, 197, 197, 197, 201, 201, 201, 197, 54, 54, 54, 10, 1, 1, 1, 1, 197, 197] 201
rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 273
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042922 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042922
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042922/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042922
Building REAL300000042923
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042923'
/scratch/stefan/7769623/working/building/REAL300000042923 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042923

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042923/0 /scratch/stefan/7769623/working/building/REAL300000042923 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1011
`/scratch/stefan/7769623/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1)

`REAL300000042923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042923 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 134, 134, 134, 134, 134, 201, 201, 201, 201, 201, 201, 134, 43, 43, 43, 8, 1, 1, 1, 1, 134, 134, 134, 134] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 594
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042923 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(S(=O)(=O)C(F)(F)F)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 62, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 1, 11, 11, 11, 62, 134, 134, 134, 134, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 292
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042923 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042923
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042923/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042923
Building REAL300000042924
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042924'
/scratch/stefan/7769623/working/building/REAL300000042924 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042924

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042924/0 /scratch/stefan/7769623/working/building/REAL300000042924 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1012
`/scratch/stefan/7769623/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)N2)=C1)

`REAL300000042924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042924 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 52, 52, 75, 75, 75, 75, 125, 125, 125, 125, 125, 75, 1, 1, 1, 1, 13, 52, 75, 75, 125, 125, 125, 125, 125, 75, 1] 125
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 36] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042924 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 125, 125, 125, 125, 90, 27, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 125, 125, 125, 125, 90, 27, 6, 7, 1, 1, 1, 1, 1, 7, 125] 125
rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36])
total number of confs: 286
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042924 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C3=CC=CC=C3)N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [75, 75, 75, 75, 74, 75, 75, 38, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 75, 74, 75, 75, 38, 6, 1, 1, 7, 7, 1, 7, 7, 1, 75] 125
rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36])
total number of confs: 165
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042924 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042924
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042924/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042924
Building REAL300000042925
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042925'
/scratch/stefan/7769623/working/building/REAL300000042925 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042925

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042925/0 /scratch/stefan/7769623/working/building/REAL300000042925 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1013
`/scratch/stefan/7769623/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)=C1)

`REAL300000042925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042925 none O=C([O-])C1=CC=CC(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 55, 55, 96, 96, 96, 96, 96, 164, 164, 164, 164, 164, 96, 1, 1, 1, 1, 11, 55, 96, 96, 164, 164, 164, 164, 1] 164
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042925 none O=C([O-])C1=CC=CC(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 164, 164, 164, 164, 164, 126, 39, 39, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 164, 164, 164, 164, 126, 39, 12, 13, 1, 1, 1, 1, 164] 164
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 399
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042925 none O=C([O-])C1=CC=CC(NN=CC2=CC=NC(C3=CC=CC=N3)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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: [96, 96, 96, 96, 95, 96, 96, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 96, 96, 96, 96, 34, 6, 1, 1, 13, 13, 12, 13, 96] 164
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 178
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042925 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042925
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042925/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042925
Building REAL300000042926
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042926'
/scratch/stefan/7769623/working/building/REAL300000042926 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042926

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042926/0 /scratch/stefan/7769623/working/building/REAL300000042926 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1014
`/scratch/stefan/7769623/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(CN=NC2=CC=CC(C(=O)[O-])=C2)=C(Br)N1)

`REAL300000042926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042926 none CC1=NC(CN=NC2=CC=CC(C(=O)[O-])=C2)=C(Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 8, 51, 51, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 2, 2, 2, 8, 8, 95, 95, 95, 95, 1] 95
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042926 none CC1=NC(CN=NC2=CC=CC(C(=O)[O-])=C2)=C(Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 95, 95, 95, 95, 95, 95, 42, 42, 1, 1, 1, 1, 95] 95
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042926 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042926/1 /scratch/stefan/7769623/working/building/REAL300000042926 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1015
`/scratch/stefan/7769623/working/3D/1015' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Br)N1)

`REAL300000042926.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042926/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042926 none CC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 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, 1, 1, 10, 10, 53, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2, 10, 52, 69, 69, 69, 68, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042926 none CC1=NC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(Br)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'Br', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [68, 68, 68, 45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 69, 68, 69, 69, 69, 45, 12, 1, 1, 1, 1, 68] 69
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042926 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042926
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042926/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042926/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042926
Building REAL300000042927
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042927'
/scratch/stefan/7769623/working/building/REAL300000042927 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042927

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042927/0 /scratch/stefan/7769623/working/building/REAL300000042927 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1016
`/scratch/stefan/7769623/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCC3(CS(=O)(=O)C3)CC2)=C1)

`REAL300000042927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042927 none O=C([O-])C1=CC=CC(N=NC2CCC3(CS(=O)(=O)C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 38] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042927 none O=C([O-])C1=CC=CC(N=NC2CCC3(CS(=O)(=O)C3)CC2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14] 14
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 38])
total number of confs: 18
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042927 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042927
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042927/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042927
Building REAL300000042928
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042928'
/scratch/stefan/7769623/working/building/REAL300000042928 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042928

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042928/0 /scratch/stefan/7769623/working/building/REAL300000042928 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1017
`/scratch/stefan/7769623/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042928 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4] 4
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 32, 30, 31] set([8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042928 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1] 4
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 13
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042928 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042928
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042928/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042928
Building REAL300000042929
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042929'
/scratch/stefan/7769623/working/building/REAL300000042929 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042929

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042929/0 /scratch/stefan/7769623/working/building/REAL300000042929 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1018
`/scratch/stefan/7769623/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1Cl)

`REAL300000042929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042929 none CC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 19, 19, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 18, 18, 18, 18, 1] 19
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 17, 18, 19, 20, 21, 22, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042929 none CC1=CC=C2C(=NNC3=CC=CC(C(=O)[O-])=C3)C(=O)NC2=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 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: [18, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 18, 18, 18, 18, 18, 18, 19, 19, 19, 18, 18, 10, 1, 1, 1, 1, 18] 19
rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042929 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042929
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042929/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042929
Building REAL300000042930
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042930'
/scratch/stefan/7769623/working/building/REAL300000042930 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042930

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042930/0 /scratch/stefan/7769623/working/building/REAL300000042930 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1019
`/scratch/stefan/7769623/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C2CCCCC2=N1)

`REAL300000042930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042930 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C2CCCCC2=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 58, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 11, 58, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1] 84
rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 33, 40, 39, 34, 16, 17, 18, 19, 20, 21, 22, 36, 26, 38] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042930 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C2CCCCC2=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 43, 12, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84] 84
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 132
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042930 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042930
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042930/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042930
Building REAL300000042931
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042931'
/scratch/stefan/7769623/working/building/REAL300000042931 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042931

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042931/0 /scratch/stefan/7769623/working/building/REAL300000042931 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1020
`/scratch/stefan/7769623/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CSC(C(F)(F)F)=N2)=C1)

`REAL300000042931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042931 none O=C([O-])C1=CC=CC(NN=CC2=CSC(C(F)(F)F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 35, 35, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 11, 35, 42, 1] 42
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26])
total number of confs: 69
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042931 none O=C([O-])C1=CC=CC(NN=CC2=CSC(C(F)(F)F)=N2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 42, 42, 42, 42, 29, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 42, 42, 42, 42, 28, 6, 1, 42] 42
rigid atoms, others: [10, 11, 12, 13, 14, 15, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27])
total number of confs: 92
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042931 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042931
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042931/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042931
Building REAL300000042932
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042932'
/scratch/stefan/7769623/working/building/REAL300000042932 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042932

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042932/0 /scratch/stefan/7769623/working/building/REAL300000042932 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1021
`/scratch/stefan/7769623/working/3D/1021' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC=C2Br)=C1)

`REAL300000042932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042932 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 35, 35, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 13, 35, 49, 49, 49, 1] 49
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042932 none O=C([O-])C1=CC=CC(NN=CC2=CC(Br)=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 37, 10, 1, 1, 1, 49] 49
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 111
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042932 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042932
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042932/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042932
Building REAL300000042933
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042933'
/scratch/stefan/7769623/working/building/REAL300000042933 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042933

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042933/0 /scratch/stefan/7769623/working/building/REAL300000042933 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1022
`/scratch/stefan/7769623/working/3D/1022' -> `0.mol2'
Preparing input files

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

`REAL300000042933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042933 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)F)C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 62, 124, 125, 125, 125, 155, 155, 125, 125, 125, 1, 1, 1, 1, 13, 62, 125, 125, 155, 125, 1] 155
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30])
total number of confs: 376
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042933 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)F)C(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 125, 125, 125, 125, 58, 11, 11, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 125, 125, 125, 125, 58, 11, 1, 1, 12, 1, 125] 155
rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 29, 31])
total number of confs: 270
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042933 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042933
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042933/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042933
Building REAL300000042934
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042934'
/scratch/stefan/7769623/working/building/REAL300000042934 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042934

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042934/0 /scratch/stefan/7769623/working/building/REAL300000042934 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1023
`/scratch/stefan/7769623/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(Cl)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Cl)

`REAL300000042934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042934 none CC1=C(Cl)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 2, 2, 2, 1, 1, 8, 30, 41, 41, 41, 41] 41
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 97
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042934 none CC1=C(Cl)C=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 37, 41, 41, 41, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 41, 41, 36, 10, 1, 1, 1, 1] 41
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042934 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042934
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042934/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042934
Building REAL300000042935
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042935'
/scratch/stefan/7769623/working/building/REAL300000042935 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042935

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042935/0 /scratch/stefan/7769623/working/building/REAL300000042935 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1024
`/scratch/stefan/7769623/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)C=C1I)

`REAL300000042935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042935 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)C=C1I NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 18, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 47, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 47, 58, 58, 58, 58, 2, 2, 2, 1] 58
rigid atoms, others: [0, 1, 2, 3, 4, 34, 16, 17, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 147
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042935 none CC1=CC(C=NNC2=CC=CC(C(=O)[O-])=C2)=C(C)C=C1I NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 18, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [58, 58, 58, 44, 44, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 58, 58, 44, 44, 58, 58, 58, 58, 44, 13, 1, 1, 1, 1, 58, 58, 58, 58] 58
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 15, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 129
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042935 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042935
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042935/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042935
Building REAL300000042936
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042936'
/scratch/stefan/7769623/working/building/REAL300000042936 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042936

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042936/0 /scratch/stefan/7769623/working/building/REAL300000042936 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1025
`/scratch/stefan/7769623/working/3D/1025' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CC=C(Br)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042936 none N#CC1=CC=C(Br)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 41, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 10, 41, 55, 55, 55, 55, 1] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28])
total number of confs: 127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042936 none N#CC1=CC=C(Br)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 55, 55, 55, 37, 37, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 55, 37, 13, 1, 1, 1, 1, 55] 55
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 29])
total number of confs: 95
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042936 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042936
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042936/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042936
Building REAL300000042937
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042937'
/scratch/stefan/7769623/working/building/REAL300000042937 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042937

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042937/0 /scratch/stefan/7769623/working/building/REAL300000042937 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1026
`/scratch/stefan/7769623/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042937 none CSCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 10, 10, 58, 118, 119, 119, 119, 119, 119, 119, 118, 1, 1, 18, 18, 18, 4, 4, 1, 1, 10, 58, 118, 119, 119, 118, 1, 1] 201
rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 19, 20, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042937 none CSCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 126, 118, 86, 118, 118, 49, 49, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 118, 118, 200, 200, 200, 126, 126, 118, 118, 49, 9, 1, 1, 1, 1, 118, 118] 201
rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 478
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042937 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042937
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042937/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042937
Building REAL300000042938
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042938'
/scratch/stefan/7769623/working/building/REAL300000042938 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042938

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042938/0 /scratch/stefan/7769623/working/building/REAL300000042938 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1027
`/scratch/stefan/7769623/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C2CCOCC2=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042938 none CN1N=C2CCOCC2=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 56, 83, 83, 83, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 55, 83, 83, 83, 83] 83
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042938 none CN1N=C2CCOCC2=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 5, 5, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 82, 81, 83, 83, 83, 83, 82, 45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 83, 83, 83, 83, 82, 83, 83, 83, 83, 45, 12, 1, 1, 1, 1] 83
rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 143
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042938 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042938
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042938/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042938
Building REAL300000042939
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042939'
/scratch/stefan/7769623/working/building/REAL300000042939 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042939

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042939/0 /scratch/stefan/7769623/working/building/REAL300000042939 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1028
`/scratch/stefan/7769623/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C(C)OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042939 none COC(=O)C(C)OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 44, 9, 22, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 60, 60, 60, 60, 60, 60, 60, 60, 44, 44, 44, 22, 22, 22, 22, 1, 1, 1, 1, 7, 25, 60, 60, 60, 60] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 254
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042939 none COC(=O)C(C)OC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 113, 145, 60, 60, 60, 28, 60, 60, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 145, 145, 145, 145, 60, 60, 60, 60, 27, 6, 1, 1, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 681
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042939 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042939
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042939/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042939
Building REAL300000042940
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042940'
/scratch/stefan/7769623/working/building/REAL300000042940 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042940

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042940/0 /scratch/stefan/7769623/working/building/REAL300000042940 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1029
`/scratch/stefan/7769623/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)COC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042940 none COC(=O)COC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [131, 131, 38, 131, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 32, 32, 32, 32, 32, 32, 32, 32, 131, 131, 131, 38, 38, 1, 1, 1, 1, 4, 17, 32, 32, 32, 32] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 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: 425
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042940 none COC(=O)COC1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 169, 201, 77, 32, 32, 32, 21, 32, 32, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 169, 169, 32, 32, 32, 32, 21, 7, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 694
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042940 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042940
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042940/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042940
Building REAL300000042941
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042941'
/scratch/stefan/7769623/working/building/REAL300000042941 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042941

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042941/0 /scratch/stefan/7769623/working/building/REAL300000042941 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1030
`/scratch/stefan/7769623/working/3D/1030' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(N=NC3=CC=CC(C(=O)[O-])=C3)C2)CC1)

`REAL300000042941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042941 none CC(C)(C)OC(=O)N1CCC2(CC(N=NC3=CC=CC(C(=O)[O-])=C3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [29, 24, 29, 29, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 30, 30, 30, 29, 29, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1] 148
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042941 none CC(C)(C)OC(=O)N1CCC2(CC(N=NC3=CC=CC(C(=O)[O-])=C3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [148, 148, 148, 148, 104, 43, 104, 43, 43, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 148, 148, 148, 148, 148, 148, 148, 148, 148, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43] 148
rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52])
total number of confs: 357
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042941 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042941
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042941/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042941
Building REAL300000042942
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042942'
/scratch/stefan/7769623/working/building/REAL300000042942 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042942

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042942/0 /scratch/stefan/7769623/working/building/REAL300000042942 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1031
`/scratch/stefan/7769623/working/3D/1031' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)C1)

`REAL300000042942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042942 none CC(C)(C)OC(=O)NCC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 52, 29, 52, 7, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56, 29, 7, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042942 none CC(C)(C)OC(=O)NCC1CCC(N=NC2=CC=CC(C(=O)[O-])=C2)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', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 196, 145, 196, 69, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 69, 69, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 22, 22] 201
rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 681
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042942 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042942
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042942/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042942
Building REAL300000042943
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042943'
/scratch/stefan/7769623/working/building/REAL300000042943 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042943

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042943/0 /scratch/stefan/7769623/working/building/REAL300000042943 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1032
`/scratch/stefan/7769623/working/3D/1032' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)=C1)

`REAL300000042943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042943 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 32, 32, 69, 69, 34, 69, 69, 69, 130, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 9, 32, 69, 69, 69, 69, 201, 201, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 468
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042943 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 169, 75, 75, 30, 30, 30, 29, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 169, 75, 30, 29, 30, 30, 1, 1, 1, 1, 201] 201
rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39])
total number of confs: 506
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042943 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2OC2=CC=CC(F)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 30, 69, 69, 69, 69, 33, 10, 1, 1, 1, 1, 30, 30, 30, 30, 69] 201
rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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
/scratch/stefan/7769623/working/building/REAL300000042943 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042943
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042943/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042943
Building REAL300000042944
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042944'
/scratch/stefan/7769623/working/building/REAL300000042944 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042944

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042944/0 /scratch/stefan/7769623/working/building/REAL300000042944 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1033
`/scratch/stefan/7769623/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br)

`REAL300000042944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042944 none COC1=CC=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 57, 138, 138, 138, 138, 138, 138, 138, 138, 1, 1, 4, 4, 4, 1, 1, 2, 2, 2, 7, 57, 138, 138, 138, 138] 138
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 250
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042944 none COC1=CC=C(C)C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1Br NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 138, 138, 138, 138, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 63, 12, 1, 1, 1, 1] 138
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 205
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042944 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042944
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042944/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042944
Building REAL300000042945
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042945'
/scratch/stefan/7769623/working/building/REAL300000042945 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042945

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042945/0 /scratch/stefan/7769623/working/building/REAL300000042945 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1034
`/scratch/stefan/7769623/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCC3=C(C=CS3)C2)=C1)

`REAL300000042945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042945 none O=C([O-])C1=CC=CC(N=NC2CCCC3=C(C=CS3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 23
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042945 none O=C([O-])C1=CC=CC(N=NC2CCCC3=C(C=CS3)C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 23])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042945 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042945
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042945/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042945
Building REAL300000042946
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042946'
/scratch/stefan/7769623/working/building/REAL300000042946 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042946

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042946/0 /scratch/stefan/7769623/working/building/REAL300000042946 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1035
`/scratch/stefan/7769623/working/3D/1035' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1)

`REAL300000042946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042946 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 60, 60, 35, 48, 178, 201, 201, 201, 201, 201, 201, 60, 60, 29, 29, 29, 6, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 60, 60] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 397
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: REAL300000042946 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 5, 39, 47, 160, 201, 201, 201, 201, 201, 201, 201, 201, 5, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 41, 47, 47, 160, 200, 201, 201, 201, 16, 16, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 549
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042946 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(OC2=CC=C(F)C=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 30, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 1, 1, 6, 6, 6, 30, 60, 60, 60, 60, 1, 1, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [1, 35, 36, 41, 42, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 137
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042946 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042946
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042946/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042946
Building REAL300000042947
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042947'
/scratch/stefan/7769623/working/building/REAL300000042947 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042947

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042947/0 /scratch/stefan/7769623/working/building/REAL300000042947 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1036
`/scratch/stefan/7769623/working/3D/1036' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=CN=C2C=C1)

`REAL300000042947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042947 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 93, 93, 93, 93, 93, 93, 93, 93, 93, 47, 47, 47, 10, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93] 93
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 153
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042947 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 58, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1] 93
rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 197
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042947 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042947
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042947/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042947
Building REAL300000042948
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042948'
/scratch/stefan/7769623/working/building/REAL300000042948 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042948

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042948/0 /scratch/stefan/7769623/working/building/REAL300000042948 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1037
`/scratch/stefan/7769623/working/3D/1037' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042948 none CN(C)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 6, 6, 24, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 6, 23, 39, 39, 39, 38, 1, 1] 47
rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 22, 38, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 101
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042948 none CN(C)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 38, 47, 32, 38, 38, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 47, 47, 47, 47, 47, 47, 39, 39, 19, 3, 1, 1, 1, 1, 39, 39] 47
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 131
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042948 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042948
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042948/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042948
Building REAL300000042949
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042949'
/scratch/stefan/7769623/working/building/REAL300000042949 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042949

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042949/0 /scratch/stefan/7769623/working/building/REAL300000042949 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1038
`/scratch/stefan/7769623/working/3D/1038' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN(CC)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042949 none CCN(CC)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 4, 6, 7, 1, 4, 1, 1, 1, 1, 1, 6, 6, 18, 29, 29, 29, 29, 29, 29, 29, 28, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 1, 1, 6, 18, 29, 29, 29, 28, 1, 1] 59
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 44, 43, 23, 24] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42])
total number of confs: 103
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042949 none CCN(CC)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [55, 45, 41, 45, 55, 28, 41, 22, 28, 28, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 29, 29, 13, 3, 1, 1, 1, 1, 28, 28] 59
rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 270
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042949 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042949
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042949/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042949
Building REAL300000042950
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042950'
/scratch/stefan/7769623/working/building/REAL300000042950 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042950

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042950/0 /scratch/stefan/7769623/working/building/REAL300000042950 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1039
`/scratch/stefan/7769623/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042950 none CCNC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 53, 133, 133, 133, 133, 133, 134, 134, 133, 1, 1, 9, 9, 9, 9, 9, 3, 1, 1, 9, 53, 133, 133, 133, 133, 1, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 22, 38, 29, 30, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042950 none CCNC(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 161, 161, 61, 161, 61, 134, 134, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 134, 134, 201, 201, 201, 201, 201, 161, 134, 133, 60, 12, 1, 1, 1, 1, 134, 134] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 909
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042950 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042950
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042950/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042950
Building REAL300000042951
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042951'
/scratch/stefan/7769623/working/building/REAL300000042951 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042951

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042951/0 /scratch/stefan/7769623/working/building/REAL300000042951 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1040
`/scratch/stefan/7769623/working/3D/1040' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C2SC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC2=C1)

`REAL300000042951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042951 none COC1=CC=C2SC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 2, 2, 2, 1, 1, 9, 50, 101, 101, 101, 101, 1, 1] 103
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 20, 21, 22, 26, 27] set([0, 32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 196
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042951 none COC1=CC=C2SC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC2=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 101, 101, 100, 101, 101, 101, 59, 59, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 101, 101, 103, 103, 103, 101, 101, 59, 12, 1, 1, 1, 1, 101, 101] 103
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 163
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042951 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042951
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042951/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042951
Building REAL300000042952
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042952'
/scratch/stefan/7769623/working/building/REAL300000042952 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042952

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042952/0 /scratch/stefan/7769623/working/building/REAL300000042952 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1041
`/scratch/stefan/7769623/working/3D/1041' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)=CC=C1)

`REAL300000042952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042952 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 10, 18, 18, 18, 1, 1, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27])
total number of confs: 39
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042952 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Cl)C(Cl)=C32)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 18, 19, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 7, 1, 1, 1, 18, 18, 18] 19
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 37
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042952 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042952
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042952/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042952
Building REAL300000042953
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042953'
/scratch/stefan/7769623/working/building/REAL300000042953 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042953

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042953/0 /scratch/stefan/7769623/working/building/REAL300000042953 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1042)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1042
`/scratch/stefan/7769623/working/3D/1042' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(C3=CC=CC=C3)=NO2)=C1)

`REAL300000042953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042953 none O=C([O-])C1=CC=CC(NN=CC2=CC(C3=CC=CC=C3)=NO2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 66, 66, 102, 102, 102, 108, 108, 102, 108, 108, 102, 102, 1, 1, 1, 1, 13, 66, 102, 108, 108, 102, 108, 108, 1] 108
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042953 none O=C([O-])C1=CC=CC(NN=CC2=CC(C3=CC=CC=C3)=NO2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 108, 107, 108, 108, 87, 22, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 108, 107, 108, 108, 87, 22, 6, 1, 1, 1, 1, 1, 108] 108
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 254
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042953 none O=C([O-])C1=CC=CC(NN=CC2=CC(C3=CC=CC=C3)=NO2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [102, 102, 102, 102, 101, 102, 102, 38, 6, 6, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 102, 101, 102, 102, 38, 6, 1, 6, 6, 1, 6, 6, 102] 108
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 188
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042953 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042953/1 /scratch/stefan/7769623/working/building/REAL300000042953 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1043)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1043
`/scratch/stefan/7769623/working/3D/1043' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NCC2=CC(C3=CC=CC=C3)=NO2)=C1)

`REAL300000042953.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042953/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042953 none O=C([O-])C1=CC=CC(N=NCC2=CC(C3=CC=CC=C3)=NO2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 160, 160, 160, 201, 201, 160, 201, 201, 160, 160, 1, 1, 1, 1, 47, 46, 160, 201, 201, 167, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 24, 25] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042953 none O=C([O-])C1=CC=CC(N=NCC2=CC(C3=CC=CC=C3)=NO2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 166, 166, 46, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 46, 46, 7, 1, 1, 1, 1, 1, 201] 201
rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 365
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042953 none O=C([O-])C1=CC=CC(N=NCC2=CC(C3=CC=CC=C3)=NO2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [160, 160, 160, 160, 160, 160, 160, 72, 72, 9, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 160, 160, 160, 160, 9, 9, 1, 7, 7, 2, 7, 7, 160] 201
rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34])
total number of confs: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042953 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042953
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042953/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042953/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042953
Building REAL300000042954
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042954'
/scratch/stefan/7769623/working/building/REAL300000042954 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042954

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042954/0 /scratch/stefan/7769623/working/building/REAL300000042954 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1044)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1044
`/scratch/stefan/7769623/working/3D/1044' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=NN1C1=CC=CC=C1)

`REAL300000042954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042954 none NC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 57, 124, 124, 124, 124, 124, 124, 124, 123, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 9, 57, 124, 124, 124, 123, 1, 6, 6, 3, 6, 6] 194
rigid atoms, others: [0, 1, 2, 3, 32, 15, 16, 17, 18, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 253
number of broken/clashed sets: 107
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042954 none NC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 36, 36, 139, 194, 194, 194, 194, 194, 194, 194, 194, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 139, 194, 194, 194, 194, 6, 1, 1, 1, 1, 1] 194
rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 427
number of broken/clashed sets: 107
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042954 none NC1=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=NN1C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [124, 123, 67, 67, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 123, 123, 123, 123, 194, 194, 193, 194, 194, 124, 124, 67, 12, 1, 1, 1, 1, 123, 194, 194, 193, 194, 194] 194
rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 333
number of broken/clashed sets: 107
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042954 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042954
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042954/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042954
Building REAL300000042955
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042955'
/scratch/stefan/7769623/working/building/REAL300000042955 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042955

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042955/0 /scratch/stefan/7769623/working/building/REAL300000042955 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1045)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1045
`/scratch/stefan/7769623/working/3D/1045' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042955 none CCC(=O)NC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 58, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 30, 30, 30, 30, 30, 5, 1, 1, 13, 13, 13, 58, 117, 117, 117, 117, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 40, 41, 22, 23, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 336
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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042955 none CCC(=O)NC1=CC=C(C(C)=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 157, 157, 157, 117, 81, 117, 117, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 117, 117, 201, 201, 201, 201, 201, 157, 117, 117, 36, 36, 36, 8, 1, 1, 1, 1, 117, 117] 201
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 725
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042955 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042955
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042955/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042955
Building REAL300000042956
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042956'
/scratch/stefan/7769623/working/building/REAL300000042956 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042956

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042956/0 /scratch/stefan/7769623/working/building/REAL300000042956 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1046)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1046
`/scratch/stefan/7769623/working/3D/1046' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC=CC(C)=C2S1)

`REAL300000042956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042956 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 53, 53, 53, 12, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85] 85
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 137
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042956 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 51, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 51, 85, 85, 85, 85, 2, 2, 2, 1, 1, 1, 2, 2, 2] 85
rigid atoms, others: [1, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40])
total number of confs: 192
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042956 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042956
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042956/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042956
Building REAL300000042957
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042957'
/scratch/stefan/7769623/working/building/REAL300000042957 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042957

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042957/0 /scratch/stefan/7769623/working/building/REAL300000042957 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1047)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1047
`/scratch/stefan/7769623/working/3D/1047' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)S2)=CC=C1)

`REAL300000042957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042957 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)S2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [2, 1, 2, 1, 1, 1, 1, 13, 13, 13, 13, 46, 46, 118, 136, 136, 136, 136, 136, 136, 136, 136, 13, 1, 1, 1, 1, 13, 13, 46, 118, 136, 136, 136, 136, 1, 1, 1] 136
rigid atoms, others: [1, 3, 4, 5, 6, 35, 23, 24, 25, 26, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 342
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042957 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)S2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 136, 136, 136, 136, 66, 66, 66, 66, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 136, 136, 136, 136, 66, 66, 31, 7, 1, 1, 1, 1, 136, 136, 136] 136
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37])
total number of confs: 202
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042957 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)S2)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 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: [13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 32, 66, 66, 66, 66, 66, 65, 66, 66, 1, 13, 13, 12, 13, 1, 1, 6, 32, 66, 65, 66, 66, 13, 13, 12] 136
rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 152
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042957 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042957
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042957/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042957
Building REAL300000042958
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042958'
/scratch/stefan/7769623/working/building/REAL300000042958 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042958

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042958/0 /scratch/stefan/7769623/working/building/REAL300000042958 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1048)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1048
`/scratch/stefan/7769623/working/3D/1048' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1)

`REAL300000042958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042958 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 49, 49, 49, 12, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91] 91
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 155
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042958 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC(C)=CC(C)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 54, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 54, 91, 91, 91, 91, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2] 91
rigid atoms, others: [1, 36, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 41, 42, 43])
total number of confs: 215
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042958 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042958
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042958/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042958
Building REAL300000042959
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042959'
/scratch/stefan/7769623/working/building/REAL300000042959 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042959

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042959/0 /scratch/stefan/7769623/working/building/REAL300000042959 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1049)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1049
`/scratch/stefan/7769623/working/3D/1049' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)(C)C)=N1)

`REAL300000042959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042959 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 65, 65, 65, 65, 71, 71, 71, 65, 39, 39, 39, 10, 1, 1, 1, 1, 65, 71, 71, 71, 71, 71, 71, 71, 71, 71] 71
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 148
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042959 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 8, 30, 65, 65, 65, 65, 65, 66, 66, 65, 1, 1, 1, 1, 1, 4, 4, 4, 1, 9, 9, 9, 30, 65, 65, 65, 65, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 71
rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 147
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042959 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042959/1 /scratch/stefan/7769623/working/building/REAL300000042959 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1050)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1050
`/scratch/stefan/7769623/working/3D/1050' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)(C)C)=N1)

`REAL300000042959.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042959/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042959 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 142, 142, 142, 142, 201, 201, 201, 142, 54, 54, 54, 54, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 646
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042959 none CC(N=NC1=CC=CC(C(=O)[O-])=C1)C1=CSC(C(C)(C)C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 75, 75, 142, 142, 142, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 13, 142, 142, 142, 142, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201
rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 234
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042959 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042959
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042959/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042959/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042959
Building REAL300000042960
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042960'
/scratch/stefan/7769623/working/building/REAL300000042960 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042960

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042960/0 /scratch/stefan/7769623/working/building/REAL300000042960 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1051)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1051
`/scratch/stefan/7769623/working/3D/1051' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=C(F)C(F)=C3Br)=CC=C1)

`REAL300000042960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042960 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=C(F)C(F)=C3Br)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 17, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 11, 17, 17, 1, 1, 1] 18
rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042960 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C2C=C(F)C(F)=C3Br)=CC=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 17, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 17, 18, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 7, 1, 1, 17, 17, 17] 18
rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 28, 29, 30])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042960 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042960
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042960/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042960
Building REAL300000042961
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042961'
/scratch/stefan/7769623/working/building/REAL300000042961 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042961

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042961/0 /scratch/stefan/7769623/working/building/REAL300000042961 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1052)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1052
`/scratch/stefan/7769623/working/3D/1052' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN(C)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042961 none CCN(C)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [21, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 6, 6, 26, 47, 47, 47, 47, 47, 48, 48, 47, 1, 1, 21, 21, 21, 21, 21, 13, 13, 13, 1, 1, 6, 26, 47, 47, 47, 47, 1, 1] 136
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 182
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042961 none CCN(C)C(=O)C1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 96, 66, 96, 32, 66, 32, 47, 47, 17, 17, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 136, 136, 136, 136, 136, 96, 96, 96, 47, 47, 17, 3, 1, 1, 1, 1, 47, 47] 136
rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 582
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042961 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042961
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042961/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042961
Building REAL300000042962
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042962'
/scratch/stefan/7769623/working/building/REAL300000042962 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042962

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042962/0 /scratch/stefan/7769623/working/building/REAL300000042962 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1053)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1053
`/scratch/stefan/7769623/working/3D/1053' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21)

`REAL300000042962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042962 none CCN1CCC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 74, 74, 74, 74, 74, 75, 75, 74, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 10, 49, 74, 74, 74, 74, 1, 1] 75
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 20, 21, 22, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042962 none CCN1CCC2=CC(C=NNC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [75, 74, 74, 74, 74, 74, 74, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 74, 74, 74, 75, 75, 75, 75, 75, 74, 74, 74, 74, 74, 43, 10, 1, 1, 1, 1, 74, 74] 75
rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40])
total number of confs: 128
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042962 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042962/1 /scratch/stefan/7769623/working/building/REAL300000042962 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1054)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1054
`/scratch/stefan/7769623/working/3D/1054' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCC2=CC(C=[NH+]NC3=CC=CC(C(=O)[O-])=C3)=CC=C21)

`REAL300000042962.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042962/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042962 none CCN1CCC2=CC(C=[NH+]NC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 13, 25, 66, 66, 66, 66, 1, 1] 66
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 21, 22, 23, 33, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39])
total number of confs: 135
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042962 none CCN1CCC2=CC(C=[NH+]NC3=CC=CC(C(=O)[O-])=C3)=CC=C21 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 25, 25, 12, 25, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 25, 12, 1, 1, 1, 1, 66, 66] 66
rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41])
total number of confs: 124
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042962 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042962
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042962/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042962/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042962
Building REAL300000042963
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042963'
/scratch/stefan/7769623/working/building/REAL300000042963 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042963

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042963/0 /scratch/stefan/7769623/working/building/REAL300000042963 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1055)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1055
`/scratch/stefan/7769623/working/3D/1055' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC=CC(Cl)=C2S1)

`REAL300000042963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042963 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC=CC(Cl)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 53, 53, 53, 12, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83] 83
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 135
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042963 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=C(C)C2=CC=CC(Cl)=C2S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 53, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 53, 83, 83, 83, 83, 2, 2, 2, 1, 1, 1] 83
rigid atoms, others: [1, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 183
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042963 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042963
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042963/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042963
Building REAL300000042964
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042964'
/scratch/stefan/7769623/working/building/REAL300000042964 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042964

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042964/0 /scratch/stefan/7769623/working/building/REAL300000042964 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1056)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1056
`/scratch/stefan/7769623/working/3D/1056' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OC(C)(C)C)

`REAL300000042964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042964 none CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [5, 1, 5, 1, 1, 1, 1, 13, 13, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 7, 7, 21, 23, 23, 23, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 39, 39, 39, 39, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 113
rigid atoms, others: [19, 1, 34, 3, 4, 5, 6, 33, 41, 42, 17, 18, 35, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 110
number of broken/clashed sets: 109
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042964 none CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OC(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [49, 39, 49, 39, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 71, 71, 112, 112, 112, 112, 49, 49, 49, 49, 49, 49, 49, 39, 39, 39, 39, 1, 1, 1, 1, 39, 39, 112, 112, 112, 112, 112, 112, 112, 112, 112] 113
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 315
number of broken/clashed sets: 109
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042964 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042964
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042964/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042964
Building REAL300000042965
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042965'
/scratch/stefan/7769623/working/building/REAL300000042965 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042965

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042965/0 /scratch/stefan/7769623/working/building/REAL300000042965 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1057)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1057
`/scratch/stefan/7769623/working/3D/1057' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC(Cl)=C1O)

`REAL300000042965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042965 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC(Cl)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 74, 74, 74, 74, 74, 74, 74, 74, 44, 44, 44, 10, 1, 1, 1, 1, 74, 74, 74, 74, 74, 148] 148
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 275
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042965 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC(Cl)=C1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 49, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 49, 74, 74, 74, 74, 1, 2, 2, 2, 1, 2] 148
rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35])
total number of confs: 171
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042965 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042965/1 /scratch/stefan/7769623/working/building/REAL300000042965 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1058)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1058
`/scratch/stefan/7769623/working/3D/1058' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC(Cl)=C1[O-])

`REAL300000042965.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042965/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042965 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC(Cl)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 8, 1, 1, 1, 1, 25, 25, 25, 25, 25] 25
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34])
total number of confs: 48
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042965 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC(C)=CC(Cl)=C1[O-] NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [5, 1, 5, 5, 17, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 25, 25, 25, 25, 1, 2, 2, 2, 1] 25
rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33])
total number of confs: 59
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042965 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042965
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042965/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042965/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042965
Building REAL300000042966
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042966'
/scratch/stefan/7769623/working/building/REAL300000042966 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042966

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042966/0 /scratch/stefan/7769623/working/building/REAL300000042966 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1059)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1059
`/scratch/stefan/7769623/working/3D/1059' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl)

`REAL300000042966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042966 none CSC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 11, 11, 57, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 9, 9, 9, 1, 1, 11, 57, 107, 107, 107, 107, 1] 147
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042966 none CSC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 106, 88, 107, 107, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 107, 107, 107, 147, 147, 147, 107, 107, 52, 12, 1, 1, 1, 1, 107] 147
rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 322
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042966 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042966
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042966/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042966
Building REAL300000042967
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042967'
/scratch/stefan/7769623/working/building/REAL300000042967 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042967

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042967/0 /scratch/stefan/7769623/working/building/REAL300000042967 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1060)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1060
`/scratch/stefan/7769623/working/3D/1060' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC2=C1CCCC(N=NC1=CC=CC(C(=O)[O-])=C1)C2)

`REAL300000042967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042967 none COC1=CC=CC2=C1CCCC(N=NC1=CC=CC(C(=O)[O-])=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 1, 1] 31
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42] set([0, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042967 none COC1=CC=CC2=C1CCCC(N=NC1=CC=CC(C(=O)[O-])=C1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 31, 31] 31
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042967 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042967
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042967/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042967
Building REAL300000042968
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042968'
/scratch/stefan/7769623/working/building/REAL300000042968 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042968

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042968/0 /scratch/stefan/7769623/working/building/REAL300000042968 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1061)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1061
`/scratch/stefan/7769623/working/3D/1061' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1Cl)

`REAL300000042968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042968 none CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 3, 3, 1, 1, 10, 10, 55, 83, 83, 83, 83, 83, 84, 84, 83, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 10, 55, 83, 83, 83, 83, 3, 3, 1] 84
rigid atoms, others: [0, 1, 2, 3, 4, 38, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042968 none CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [83, 83, 83, 77, 73, 83, 83, 47, 47, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 83, 83, 83, 83, 83, 84, 84, 84, 83, 83, 47, 12, 1, 1, 1, 1, 83, 84, 83] 84
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 189
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042968 none CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C=C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 40, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 3, 3, 3, 4, 4, 4, 1, 1, 6, 39, 84, 84, 84, 83, 1, 1, 3] 84
rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 36, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042968 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042968
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042968/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042968
Building REAL300000042969
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042969'
/scratch/stefan/7769623/working/building/REAL300000042969 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042969

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042969/0 /scratch/stefan/7769623/working/building/REAL300000042969 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1062)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1062
`/scratch/stefan/7769623/working/3D/1062' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(C)=C2)C=C1)

`REAL300000042969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042969 none CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(C)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 2, 2, 30, 30, 77, 108, 108, 108, 108, 108, 108, 108, 108, 6, 6, 6, 1, 1, 2, 2, 2, 6, 6, 30, 77, 108, 108, 108, 108, 7, 7, 7, 6, 1, 1] 108
rigid atoms, others: [0, 1, 2, 3, 4, 40, 41, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042969 none CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(C)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 77, 67, 78, 78, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 78, 78, 78, 108, 108, 108, 108, 108, 78, 78, 49, 12, 1, 1, 1, 1, 78, 78, 78, 78, 108, 108] 108
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41])
total number of confs: 226
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042969 none CC1=NN(C2=CC=C(C=NNC3=CC=CC(C(=O)[O-])=C3)C(C)=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 44, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 6, 6, 7, 7, 7, 1, 1, 13, 44, 78, 78, 78, 78, 2, 2, 2, 1, 6, 6] 108
rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 20, 21, 22, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042969 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042969
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042969/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042969
Building REAL300000042970
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042970'
/scratch/stefan/7769623/working/building/REAL300000042970 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042970

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042970/0 /scratch/stefan/7769623/working/building/REAL300000042970 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1063)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1063
`/scratch/stefan/7769623/working/3D/1063' -> `0.mol2'
Preparing input files

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

`REAL300000042970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042970 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)C(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 56, 56, 72, 72, 56, 72, 106, 106, 106, 106, 106, 106, 72, 72, 1, 1, 1, 1, 13, 56, 72, 72, 72, 72, 1] 106
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 380
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042970 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(F)(F)C(F)(F)F)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 72, 72, 72, 72, 72, 72, 23, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 1, 1, 72, 72, 72, 72, 23, 3, 1, 1, 1, 1, 72] 106
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042970 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042970
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042970/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042970
Building REAL300000042971
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042971'
/scratch/stefan/7769623/working/building/REAL300000042971 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042971

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042971/0 /scratch/stefan/7769623/working/building/REAL300000042971 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1064)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1064
`/scratch/stefan/7769623/working/3D/1064' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042971 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 11, 11, 46, 77, 77, 77, 77, 77, 77, 77, 77, 2, 2, 2, 1, 7, 7, 1, 1, 11, 46, 77, 77, 77, 77] 107
rigid atoms, others: [0, 1, 2, 3, 4, 32, 10, 11, 12, 13, 28, 31] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042971 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [77, 77, 77, 46, 53, 107, 107, 107, 107, 107, 77, 77, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 77, 77, 77, 107, 107, 77, 77, 46, 12, 1, 1, 1, 1] 107
rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 282
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042971 none CC1=CC(N2C=C(Cl)C=N2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 16, 1, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 21, 21, 79, 107, 107, 107, 107, 107, 107, 107, 107, 7, 7, 7, 7, 1, 1, 7, 7, 21, 79, 107, 107, 107, 107] 107
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 261
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042971 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042971
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042971/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042971
Building REAL300000042972
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042972'
/scratch/stefan/7769623/working/building/REAL300000042972 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042972

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042972/0 /scratch/stefan/7769623/working/building/REAL300000042972 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1065)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1065
`/scratch/stefan/7769623/working/3D/1065' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042972 none CCNC(=O)C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 104, 104, 104, 104, 104, 104, 104, 104, 40, 40, 40, 40, 40, 11, 1, 1, 1, 1, 10, 49, 104, 104, 104, 104] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042972 none CCNC(=O)C1=CC=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 165, 165, 104, 165, 104, 104, 104, 104, 104, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 165, 104, 104, 104, 104, 31, 9, 1, 1, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 583
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042972 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042972
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042972/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042972
Building REAL300000042973
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042973'
/scratch/stefan/7769623/working/building/REAL300000042973 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042973

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042973/0 /scratch/stefan/7769623/working/building/REAL300000042973 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1066)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1066
`/scratch/stefan/7769623/working/3D/1066' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)=C1)

`REAL300000042973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042973 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 7, 32, 32, 55, 55, 55, 55, 55, 55, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 7, 32, 55, 55, 55, 55, 78, 78, 78, 78, 1] 78
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([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])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042973 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 78, 78, 78, 61, 24, 24, 7, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 61, 24, 7, 7, 7, 7, 1, 1, 1, 1, 78] 78
rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 181
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042973 none O=C([O-])C1=CC=CC(NN=CC2=CC=CC=C2C2=CC=CC=C2Cl)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 55, 55, 55, 55, 55, 55, 37, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 55, 55, 55, 55, 37, 10, 1, 1, 1, 1, 7, 7, 2, 7, 55] 78
rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 136
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042973 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042973
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042973/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042973
Building REAL300000042974
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042974'
/scratch/stefan/7769623/working/building/REAL300000042974 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042974

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042974/0 /scratch/stefan/7769623/working/building/REAL300000042974 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1067)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1067
`/scratch/stefan/7769623/working/3D/1067' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042974 none CCC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 9, 9, 54, 94, 95, 95, 94, 94, 95, 95, 94, 1, 8, 8, 8, 7, 7, 1, 9, 54, 95, 95, 95, 94] 143
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31])
total number of confs: 223
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042974 none CCC1=CC(Br)=C(C=NNC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 94, 94, 94, 94, 94, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 94, 143, 143, 143, 143, 142, 94, 52, 12, 1, 1, 1, 1] 143
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 435
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042974 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042974
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042974/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042974
Building REAL300000042975
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042975'
/scratch/stefan/7769623/working/building/REAL300000042975 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042975

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042975/0 /scratch/stefan/7769623/working/building/REAL300000042975 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1068)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1068
`/scratch/stefan/7769623/working/3D/1068' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C12CCOCC2)

`REAL300000042975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042975 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C12CCOCC2 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 40, 40, 13, 7, 13, 1, 1, 1, 1, 1, 7, 7, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 1, 1, 1, 1, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1] 171
rigid atoms, others: [7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45])
total number of confs: 126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042975 none CC(C)(C)OC(=O)NC1CC(N=NC2=CC=CC(C(=O)[O-])=C2)C12CCOCC2 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 157, 122, 157, 42, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 42, 42, 42, 42, 42, 171, 171, 171, 171, 171, 171, 171, 171, 171, 122, 42, 42, 42, 42, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42] 171
rigid atoms, others: [45, 44, 42, 43, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49, 50, 51, 52, 53])
total number of confs: 478
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042975 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042975
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042975/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042975
Building REAL300000042976
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042976'
/scratch/stefan/7769623/working/building/REAL300000042976 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042976

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042976/0 /scratch/stefan/7769623/working/building/REAL300000042976 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1069)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1069
`/scratch/stefan/7769623/working/3D/1069' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC2=C(C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)O2)N1)

`REAL300000042976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042976 none COC(=O)C1=CC2=C(C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)O2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 4, 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: [2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 47, 47, 47, 47, 47, 48, 48, 47, 1, 1, 3, 3, 3, 1, 1, 6, 26, 47, 47, 47, 47, 1] 73
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 112
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042976 none COC(=O)C1=CC2=C(C=C(C=NNC3=CC=CC(C(=O)[O-])=C3)O2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 4, 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: [72, 73, 47, 73, 47, 47, 47, 47, 47, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 47, 73, 73, 73, 47, 47, 38, 10, 1, 1, 1, 1, 47] 73
rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042976 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042976
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042976/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042976
Building REAL300000042977
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042977'
/scratch/stefan/7769623/working/building/REAL300000042977 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042977

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042977/0 /scratch/stefan/7769623/working/building/REAL300000042977 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1070)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1070
`/scratch/stefan/7769623/working/3D/1070' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1)

`REAL300000042977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042977 none COCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 44, 26, 8, 1, 1, 1, 1, 1, 1, 6, 6, 24, 47, 47, 47, 47, 47, 48, 48, 47, 1, 83, 83, 83, 44, 44, 26, 26, 1, 1, 6, 24, 47, 47, 47, 47] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042977 none COCCOC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 147, 69, 47, 47, 47, 47, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 201, 201, 201, 201, 201, 147, 147, 47, 47, 28, 8, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 756
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042977 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042977
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042977/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042977
Building REAL300000042978
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042978'
/scratch/stefan/7769623/working/building/REAL300000042978 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042978

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042978/0 /scratch/stefan/7769623/working/building/REAL300000042978 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1071)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1071
`/scratch/stefan/7769623/working/3D/1071' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042978 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 66, 93, 93, 92, 93, 93, 93, 93, 93, 4, 4, 4, 1, 1, 1, 12, 66, 93, 93, 92, 93] 93
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 214
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042978 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 93, 93, 93, 93, 93, 93, 35, 9, 1, 1, 1, 1] 93
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 133
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042978 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042978
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042978/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042978
Building REAL300000042979
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042979'
/scratch/stefan/7769623/working/building/REAL300000042979 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042979

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042979/0 /scratch/stefan/7769623/working/building/REAL300000042979 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1072)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1072
`/scratch/stefan/7769623/working/3D/1072' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)C2=C1)

`REAL300000042979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042979 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 4, 14, 19, 19, 19, 19, 1] 19
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042979 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC(C(=O)[O-])=CC=C3)C2=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 19] 19
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042979 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042979
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042979/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042979
Building REAL300000042980
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042980'
/scratch/stefan/7769623/working/building/REAL300000042980 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042980

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042980/0 /scratch/stefan/7769623/working/building/REAL300000042980 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1073)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1073
`/scratch/stefan/7769623/working/3D/1073' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCCCC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042980 none CC(CCCCC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 5, 3, 1, 1, 1, 1, 1, 1, 1, 40, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 40, 40, 40, 40, 11, 11, 7, 7, 5, 5, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201] 201
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43])
total number of confs: 407
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042980 none CC(CCCCC1=CC=CC=C1)N=NC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 42, 91, 110, 150, 200, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 42, 42, 42, 95, 95, 106, 110, 158, 158, 196, 200, 201, 201, 201, 201, 201, 1, 1, 1, 1] 201
rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 944
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042980 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042980
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042980/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042980
Building REAL300000042981
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042981'
/scratch/stefan/7769623/working/building/REAL300000042981 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042981

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042981/0 /scratch/stefan/7769623/working/building/REAL300000042981 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1074)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1074
`/scratch/stefan/7769623/working/3D/1074' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1=NN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1)

`REAL300000042981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042981 none CC(C)(C)C1=NN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 8, 74, 75, 151, 151, 151, 151, 151, 151, 151, 151, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 151, 151, 151, 151] 190
rigid atoms, others: [1, 4, 5, 6, 7, 8, 20] set([0, 2, 3, 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: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042981 none CC(C)(C)C1=NN=C(CN=NC2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [190, 150, 190, 190, 150, 150, 150, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 150, 190, 190, 190, 190, 190, 190, 190, 190, 190, 54, 54, 1, 1, 1, 1] 190
rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 544
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042981 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042981
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042981/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042981
Building REAL300000042982
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042982'
/scratch/stefan/7769623/working/building/REAL300000042982 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042982

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042982/0 /scratch/stefan/7769623/working/building/REAL300000042982 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1075)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1075
`/scratch/stefan/7769623/working/3D/1075' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)C=C2O)=C1)

`REAL300000042982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042982 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 34, 34, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 12, 34, 51, 51, 102, 1] 102
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 186
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042982 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)C=C2O)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 50, 51, 51, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 50, 51, 51, 40, 10, 1, 1, 2, 51] 102
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27, 28])
total number of confs: 126
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042982 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042982/1 /scratch/stefan/7769623/working/building/REAL300000042982 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1076)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1076
`/scratch/stefan/7769623/working/3D/1076' -> `1.mol2'
Preparing input files

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

`REAL300000042982.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042982/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042982 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)C=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 7, 11, 11, 11, 1] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26])
total number of confs: 22
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042982 none O=C([O-])C1=CC=CC(NN=CC2=NC=C(Br)C=C2[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 8, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 10, 11, 11, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 10, 11, 11, 9, 3, 1, 1, 11] 11
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042982 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042982
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042982/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042982/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042982
Building REAL300000042983
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042983'
/scratch/stefan/7769623/working/building/REAL300000042983 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042983

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042983/0 /scratch/stefan/7769623/working/building/REAL300000042983 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1077)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1077
`/scratch/stefan/7769623/working/3D/1077' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C(C)C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042983 none CC1=NN(C(C)C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 12, 12, 36, 66, 66, 66, 66, 66, 66, 66, 66, 2, 2, 2, 5, 6, 6, 6, 5, 5, 5, 2, 2, 2, 12, 35, 66, 66, 66, 66] 66
rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 165
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042983 none CC1=NN(C(C)C)C(C)=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 66, 66, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 28, 6, 1, 1, 1, 1] 66
rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 101
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042983 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042983
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042983/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042983
Building REAL300000042984
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042984'
/scratch/stefan/7769623/working/building/REAL300000042984 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042984

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042984/0 /scratch/stefan/7769623/working/building/REAL300000042984 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1078)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1078
`/scratch/stefan/7769623/working/3D/1078' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(CC(C)C)S1)

`REAL300000042984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042984 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(CC(C)C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 147, 147, 147, 147, 194, 201, 201, 147, 49, 49, 49, 10, 1, 1, 1, 1, 147, 147, 194, 194, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 496
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042984 none CC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(CC(C)C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 64, 147, 147, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 4, 7, 7, 1, 13, 13, 13, 64, 147, 147, 147, 147, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [1, 13, 14, 15, 16, 17, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 301
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042984 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042984
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042984/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042984
Building REAL300000042985
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042985'
/scratch/stefan/7769623/working/building/REAL300000042985 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042985

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042985/0 /scratch/stefan/7769623/working/building/REAL300000042985 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1079)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1079
`/scratch/stefan/7769623/working/3D/1079' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=CC2=C(N1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=C2)

`REAL300000042985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042985 none COC(=O)C1=CC2=C(N1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 51, 51, 51, 51, 51, 51, 51, 50, 1, 7, 6, 6, 1, 1, 6, 31, 51, 51, 51, 50, 1] 83
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 23, 27, 28] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042985 none COC(=O)C1=CC2=C(N1)SC(C=NNC1=CC=CC(C(=O)[O-])=C1)=C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [82, 82, 50, 83, 50, 50, 50, 50, 50, 50, 35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 83, 82, 82, 51, 50, 35, 10, 1, 1, 1, 1, 51] 83
rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 222
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042985 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042985
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042985/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042985
Building REAL300000042986
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042986'
/scratch/stefan/7769623/working/building/REAL300000042986 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042986

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042986/0 /scratch/stefan/7769623/working/building/REAL300000042986 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1080)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1080
`/scratch/stefan/7769623/working/3D/1080' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2)=C1)

`REAL300000042986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042986 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 1, 1, 1, 1, 1, 1, 13, 35, 35, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 13, 35, 69, 69, 69, 1] 69
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042986 none O=C([O-])C1=CC=CC(NN=CC2=CC(Cl)=CC(Br)=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 69, 68, 69, 69, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 68, 69, 69, 46, 10, 1, 1, 1, 69] 69
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 149
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042986 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042986
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042986/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042986
Building REAL300000042987
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042987'
/scratch/stefan/7769623/working/building/REAL300000042987 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042987

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042987/0 /scratch/stefan/7769623/working/building/REAL300000042987 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1081)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1081
`/scratch/stefan/7769623/working/3D/1081' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1)

`REAL300000042987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042987 none CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 17, 17, 48, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 17, 48, 62, 62, 62, 62, 2, 2, 2, 1] 62
rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 159
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042987 none CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 42, 42, 42, 42, 42, 42, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 62, 62, 62, 62, 62, 62, 62, 62, 42, 42, 42, 42, 27, 7, 1, 1, 1, 1, 62, 62, 62, 62] 62
rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44])
total number of confs: 110
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042987 none CC1=CC=C(C2=CC=CC=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 29, 42, 42, 42, 42, 5, 5, 5, 5] 62
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 97
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042987 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042987
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042987/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042987
Building REAL300000042988
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042988'
/scratch/stefan/7769623/working/building/REAL300000042988 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042988

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042988/0 /scratch/stefan/7769623/working/building/REAL300000042988 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1082)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1082
`/scratch/stefan/7769623/working/3D/1082' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CN=C(CC(F)(F)F)S2)=C1)

`REAL300000042988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042988 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(CC(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 62, 130, 130, 130, 130, 201, 201, 201, 201, 130, 1, 1, 1, 1, 13, 62, 130, 201, 201, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042988 none O=C([O-])C1=CC=CC(NN=CC2=CN=C(CC(F)(F)F)S2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 5, 15, 15, 15, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 130, 130, 130, 130, 130, 53, 11, 11, 1, 1, 1, 1, 1, 1, 8, 9, 8, 9, 1, 130, 130, 130, 130, 53, 11, 1, 8, 8, 130] 201
rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30])
total number of confs: 258
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042988 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042988
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042988/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042988
Building REAL300000042989
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042989'
/scratch/stefan/7769623/working/building/REAL300000042989 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042989

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042989/0 /scratch/stefan/7769623/working/building/REAL300000042989 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1083)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1083
`/scratch/stefan/7769623/working/3D/1083' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1)

`REAL300000042989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042989 none O=C([O-])C1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 26, 26, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 6, 26, 44, 44, 44, 1] 44
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 71
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042989 none O=C([O-])C1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 36, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 44, 44, 44, 44, 36, 12, 1, 1, 1, 44] 44
rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 109
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042989 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042989
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042989/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042989
Building REAL300000042990
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042990'
/scratch/stefan/7769623/working/building/REAL300000042990 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300000042990

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042990/0 /scratch/stefan/7769623/working/building/REAL300000042990 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1084)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1084
`/scratch/stefan/7769623/working/3D/1084' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)=C1)

`REAL300000042990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042990 none COC1=CC=CC(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 13, 56, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 3, 3, 3, 1, 1, 1, 13, 56, 56, 201, 201, 201, 201, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24, 38, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042990 none COC1=CC=CC(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 66, 65, 65, 65, 14, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 65, 201, 201, 201, 201, 201, 201, 201, 65, 14, 14, 1, 1, 1, 1, 201] 201
rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 286
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042990 none COC1=CC=CC(C2=CSC(CN=NC3=CC=CC(C(=O)[O-])=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 8, 47, 47, 66, 66, 66, 66, 66, 66, 66, 66, 1, 13, 20, 20, 20, 12, 13, 13, 1, 8, 8, 66, 66, 66, 66, 13] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042990 /scratch/stefan/7769623/working /scratch/stefan/7769623
mkdir: created directory `1'
/scratch/stefan/7769623/working/building/REAL300000042990/1 /scratch/stefan/7769623/working/building/REAL300000042990 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 1 (index: 1085)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1085
`/scratch/stefan/7769623/working/3D/1085' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CC(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)=C1)

`REAL300000042990.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300000042990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042990/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042990 none COC1=CC=CC(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 13, 13, 13, 53, 53, 155, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 3, 3, 3, 1, 1, 1, 13, 53, 155, 201, 201, 201, 201, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24, 38, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042990 none COC1=CC=CC(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 52, 52, 52, 52, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 201, 201, 201, 201, 201, 201, 201, 52, 23, 5, 1, 1, 1, 1, 201] 201
rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 267
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042990 none COC1=CC=CC(C2=CSC(C=NNC3=CC=CC(C(=O)[O-])=C3)=N2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 31, 52, 52, 52, 52, 52, 52, 52, 52, 1, 13, 25, 25, 25, 12, 13, 13, 1, 7, 31, 52, 52, 52, 52, 13] 201
rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 145
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042990 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042990
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042990/0.*
1: /scratch/stefan/7769623/working/building/REAL300000042990/1.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042990
Building REAL300000042991
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042991'
/scratch/stefan/7769623/working/building/REAL300000042991 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042991

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042991/0 /scratch/stefan/7769623/working/building/REAL300000042991 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1086)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1086
`/scratch/stefan/7769623/working/3D/1086' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])=C1)

`REAL300000042991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042991 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 49, 49, 57, 57, 51, 53, 57, 57, 57, 57, 57, 1, 1, 1, 1, 13, 49, 57, 57, 57, 1] 57
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29])
total number of confs: 116
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042991 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(Cl)C=C2[N+](=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 57, 57, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 57, 57, 57, 57, 31, 7, 1, 1, 1, 57] 57
rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042991 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042991
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042991/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042991
Building REAL300000042992
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042992'
/scratch/stefan/7769623/working/building/REAL300000042992 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042992

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042992/0 /scratch/stefan/7769623/working/building/REAL300000042992 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1087)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1087
`/scratch/stefan/7769623/working/3D/1087' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042992 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 2, 6, 6, 1, 1, 13, 13, 73, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 2, 2, 2, 1, 6, 6, 6, 6, 13, 73, 159, 159, 159, 159, 1, 1] 166
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 44, 14, 15, 43, 27, 28] set([8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 311
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: REAL300000042992 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [159, 159, 159, 159, 159, 159, 159, 159, 166, 166, 166, 166, 166, 166, 74, 74, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 159, 159, 159, 159, 159, 159, 166, 166, 166, 166, 74, 13, 1, 1, 1, 1, 159, 159] 166
rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44])
total number of confs: 243
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042992 none CC1=CN2C(=NC(C3=CC=C(F)C=C3)=C2C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 117, 166, 166, 166, 166, 166, 166, 166, 166, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 31, 117, 166, 166, 166, 166, 6, 6] 166
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 370
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042992 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042992
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042992/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042992
Building REAL300000042993
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042993'
/scratch/stefan/7769623/working/building/REAL300000042993 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042993

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042993/0 /scratch/stefan/7769623/working/building/REAL300000042993 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1088)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1088
`/scratch/stefan/7769623/working/3D/1088' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(O)=C1OC)

`REAL300000042993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042993 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(O)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 6, 22, 43, 43, 43, 43, 2, 5, 5, 5] 106
rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 102
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042993 none COC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C(O)=C1OC NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [53, 43, 43, 43, 43, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 43, 43, 43, 53, 53, 53, 53, 43, 43, 27, 9, 1, 1, 1, 1, 86, 53, 53, 53] 106
rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 202
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042993 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042993
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042993/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042993
Building REAL300000042994
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042994'
/scratch/stefan/7769623/working/building/REAL300000042994 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042994

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042994/0 /scratch/stefan/7769623/working/building/REAL300000042994 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1089)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1089
`/scratch/stefan/7769623/working/3D/1089' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1)

`REAL300000042994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042994 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [89, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 105, 105, 89, 98, 105, 105, 105, 105, 105, 89, 89, 89, 89, 89, 10, 1, 1, 1, 1, 105, 105, 105, 105] 118
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 465
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042994 none CCC(=NNC1=CC=CC(C(=O)[O-])=C1)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [21, 6, 1, 6, 6, 43, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 21, 21, 21, 21, 21, 43, 105, 105, 105, 105, 1, 1, 1, 1] 118
rigid atoms, others: [2, 35, 36, 37, 34, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 259
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042994 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042994
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042994/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042994
Building REAL300000042995
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042995'
/scratch/stefan/7769623/working/building/REAL300000042995 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042995

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042995/0 /scratch/stefan/7769623/working/building/REAL300000042995 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1090)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1090
`/scratch/stefan/7769623/working/3D/1090' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=C1)

`REAL300000042995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042995 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 51, 51, 37, 20, 37, 4, 1, 1, 1, 1, 1, 1, 6, 6, 21, 37, 37, 37, 37, 37, 38, 38, 37, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 20, 4, 4, 1, 1, 6, 21, 37, 37, 37, 37, 1, 1] 201
rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 47, 48, 40, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042995 none CC(C)(C)OC(=O)NCC1=CC=C(C=NNC2=CC=CC(C(=O)[O-])=C2)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 190, 150, 190, 64, 38, 26, 38, 37, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 38, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 64, 64, 38, 37, 14, 3, 1, 1, 1, 1, 38, 38] 201
rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48])
total number of confs: 668
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042995 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042995
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042995/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042995
Building REAL300000042996
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042996'
/scratch/stefan/7769623/working/building/REAL300000042996 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042996

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042996/0 /scratch/stefan/7769623/working/building/REAL300000042996 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1091)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1091
`/scratch/stefan/7769623/working/3D/1091' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1=C2COCCN2C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1)

`REAL300000042996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042996 none COC(=O)C1=C2COCCN2C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 46, 46, 46, 46, 46, 47, 47, 46, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 7, 30, 46, 46, 46, 46, 1] 78
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 40, 24, 28, 29, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042996 none COC(=O)C1=C2COCCN2C(C=NNC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [77, 77, 46, 77, 46, 46, 46, 46, 46, 46, 46, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 78, 78, 78, 46, 46, 46, 46, 46, 46, 24, 6, 1, 1, 1, 1, 46] 78
rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 205
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042996 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042996
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042996/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042996
Building REAL300000042997
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042997'
/scratch/stefan/7769623/working/building/REAL300000042997 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042997

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042997/0 /scratch/stefan/7769623/working/building/REAL300000042997 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1092)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1092
`/scratch/stefan/7769623/working/3D/1092' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)=C1)

`REAL300000042997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042997 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 24, 24, 16, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 4, 16, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 158
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: REAL300000042997 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 47, 27, 26, 7, 6, 14, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 47, 25, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50] 50
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 43, 44, 45])
total number of confs: 161
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042997 none O=C([O-])C1=CC=CC(NN=CC2=CC=C(C(=O)N3CCCCC3)C=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 24, 24, 24, 24, 24, 15, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 1, 1, 24, 24, 24, 24, 15, 3, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 24] 50
rigid atoms, others: [32, 43, 44, 10, 11, 12, 13, 14, 15, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45])
total number of confs: 79
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042997 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042997
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042997/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042997
Building REAL300000042998
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042998'
/scratch/stefan/7769623/working/building/REAL300000042998 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042998

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042998/0 /scratch/stefan/7769623/working/building/REAL300000042998 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1093)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1093
`/scratch/stefan/7769623/working/3D/1093' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1)

`REAL300000042998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042998 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 13, 13, 44, 68, 68, 68, 68, 68, 68, 68, 68, 2, 2, 2, 1, 7, 7, 7, 1, 1, 13, 44, 68, 68, 68, 68] 130
rigid atoms, others: [0, 1, 2, 3, 4, 32, 9, 10, 11, 12, 27, 31] set([5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 162
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042998 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 68, 68, 65, 67, 130, 130, 130, 130, 68, 68, 41, 41, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 68, 68, 68, 130, 130, 130, 68, 68, 41, 12, 1, 1, 1, 1] 130
rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 246
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042998 none CC1=CC(N2C=CN=C2)=CC=C1C=NNC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 35, 40, 98, 130, 130, 130, 130, 130, 130, 130, 130, 7, 7, 7, 7, 1, 1, 1, 7, 7, 32, 98, 130, 130, 130, 130] 130
rigid atoms, others: [3, 4, 5, 6, 7, 8, 28, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 317
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042998 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042998
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042998/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042998
Building REAL300000042999
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000042999'
/scratch/stefan/7769623/working/building/REAL300000042999 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000042999

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000042999/0 /scratch/stefan/7769623/working/building/REAL300000042999 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1094)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1094
`/scratch/stefan/7769623/working/3D/1094' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OCC1=CC=CC=C1)

`REAL300000042999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000042999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000042999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042999 none CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 3, 3, 7, 32, 63, 63, 39, 63, 63, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 30, 30, 30, 30, 1, 1, 32, 32, 63, 63, 63, 63, 63] 201
rigid atoms, others: [1, 3, 4, 5, 38, 39, 44, 45, 17, 18, 19, 36, 6, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 302
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042999 none CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 63, 37, 19, 37, 3, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 201, 201, 201, 201, 63, 63, 3, 3, 1, 1, 1, 1, 1] 201
rigid atoms, others: [48, 49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 368
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000042999 none CC(C)C1CC(N=NC2=CC=CC(C(=O)[O-])=C2)CN1C(=O)OCC1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 30, 31, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 45, 45, 73, 201, 201, 201, 201, 201, 201, 31, 31, 31, 31, 31, 31, 31, 30, 30, 30, 30, 1, 1, 1, 1, 30, 30, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [43, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 693
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000042999 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000042999
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000042999/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000042999
Building REAL300000043000
mkdir: created directory `/scratch/stefan/7769623/working/building/REAL300000043000'
/scratch/stefan/7769623/working/building/REAL300000043000 /scratch/stefan/7769623/working /scratch/stefan/7769623
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300000043000

mkdir: created directory `0'
/scratch/stefan/7769623/working/building/REAL300000043000/0 /scratch/stefan/7769623/working/building/REAL300000043000 /scratch/stefan/7769623/working /scratch/stefan/7769623
Protomer 0 (index: 1095)
Found valid previously generated 3D confromation in /scratch/stefan/7769623/working/3D/1095
`/scratch/stefan/7769623/working/3D/1095' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2)=C1)

`REAL300000043000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300000043000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7769623/working/building/REAL300000043000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000043000 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 23, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 32
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000043000 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 8, 8, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 13] 13
rigid atoms, others: [39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44])
total number of confs: 22
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300000043000 none O=C([O-])C1=CC=CC(N=NC2CCCCCC2C2=CC=CC=C2)=C1 NO_LONG_NAME
dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 13] 13
rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 39, 40, 41, 42, 43, 44])
total number of confs: 25
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7769623/working/building/REAL300000043000 /scratch/stefan/7769623/working /scratch/stefan/7769623

Finished preparing REAL300000043000
Recording results
/scratch/stefan/7769623/working /scratch/stefan/7769623
Appending to /scratch/stefan/7769623/finished/xaaaabq.*
0: /scratch/stefan/7769623/working/building/REAL300000043000/0.*
Removing working files in /scratch/stefan/7769623/working/building/REAL300000043000
/scratch/stefan/7769623
Compressing combined databse files
/scratch/stefan/7769623/finished/xaaaabq.db2.gz
/scratch/stefan/7769623/finished/xaaaabq.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7769623/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7769623/working/3D/1096'
removed directory: `/scratch/stefan/7769623/working/3D'
`/scratch/stefan/7769623/working/protonate' -> `/scratch/stefan/7769623/archive'
`/scratch/stefan/7769623/working/input-smiles.ism' -> `/scratch/stefan/7769623/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7769623/working/building'
rmdir: removing directory, `/scratch/stefan/7769623/working'
ls: No match.
ls: No match.