ADL: Possible mis-conversion with prepare-ligand4

Ruth Huey rhuey at scripps.edu
Tue Mar 4 10:08:08 PST 2014


Hi,
Your receptor file, 3rrq.pdb, has alternate location coordinates A and B for some atoms.
For example:
ATOM    492  NE AARG A 104     -14.475  32.923  8.527  0.50 50.48           N  
ATOM    493  NE BARG A 104     -14.513  32.816   6.791  0.50 44.91           N  
(For more information, see: http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/coordinates.html)

BEFORE using prepare_receptor4.py,  split 3rrq.pdb into 2 new files, each containing a single set of coordinates for each atom.
Use the script, prepare_pdb_split_alt_confs.py (in AutoDockTools/Utilities24)  to create new pdb files.
Each will contain a single set of coordinates for each atom. 
Here i have symbolic links to:
   -pythonsh in the 'bin' directory of my local copy of mgltoolspckgs 
and 
   -prepare_pdb_split_alt_confs.py  (and prepare_receptor4.py) in my local AutoDockTools/Utilities24

./pythonsh ./prepare_pdb_split_alt_confs.py -r 3rrq.pdb

This creates 2 pdb files:
     3rrq_A.pdb
     3rrq_B.pdb

Either of these can be converted to pdbqt format with AutoDockTools/Utilities24/prepare_receptor4.py:
./pythonsh ./prepare_receptor4.py -r 3rrq_A.pdb -A checkhydrogens  

     Best wishes,
        Ruth   
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of Aaron Schweiger [aaron.schweiger at gmail.com]
Sent: Tuesday, March 04, 2014 4:45 AM
To: autodock at scripps.edu
Subject: ADL: Possible mis-conversion with prepare-ligand4

Hi,

The following:

# wget -O 3RRQ.pdb '
http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3RRQ
'

# ./prepare_receptor4.py -r 3RRQ.pdb -A checkhydrogens
adding gasteiger charges to peptide

Results in something unexpected around lines 603 and 902 -- specifically
lines like "HH1A1ARG"  appears to have incorrect alignment/formatting.

# grep -A 4 -B 4 -E ' (608|902) ' 3RRQ.pdbqt
ATOM    604  NE BARG A 104     -14.513  32.816   6.791  0.50 44.91
 -0.227 N
ATOM    605  HE BARG A 104     -13.871  33.606   6.857  1.00  0.00
0.177 HD
ATOM    606  CZ AARG A 104     -13.432  33.728   8.353  0.50 51.30
0.665 C
ATOM    607  CZ BARG A 104     -14.885  32.396   5.591  0.50 44.55
0.665 C
ATOM    608  NH1AARG A 104     -12.799  34.240   9.403  0.50 53.43
 -0.235 N
*ATOM    609  HH1A1ARG A 104     -11.998  34.858   9.269  1.00  0.00
0.174 HD*
*ATOM    610  HH1A2ARG A 104     -13.106  34.010  10.348  1.00  0.00
0.174 HD*
ATOM    611  NH1BARG A 104     -15.729  31.374   5.501  0.50 40.79
 -0.235 N
ATOM    612  HH1B1ARG A 104     -16.087  30.924   6.343  1.00  0.00
0.174 HD
--
ATOM    898  OE1AGLN A 133     -31.964  20.646  17.323  0.50 77.84
 -0.274 OA
ATOM    899  OE1BGLN A 133     -30.712  24.655  17.803  0.50 75.13
 -0.274 OA
ATOM    900  NE2AGLN A 133     -31.226  20.448  15.216  0.50 71.43
 -0.370 N
*ATOM    901  HE2A1GLN A 133     -30.607  20.751  14.464  1.00  0.00
0.159 HD*
*ATOM    902  HE2A2GLN A 133     -31.882  19.679  15.079  1.00  0.00
0.159 HD*
ATOM    903  NE2BGLN A 133     -29.047  25.776  18.801  0.50 76.82
 -0.370 N
ATOM    904  HE2B1GLN A 133     -29.641  26.605  18.817  1.00  0.00
0.159 HD
ATOM    905  HE2B2GLN A 133     -28.102  25.799  19.183  1.00  0.00
0.159 HD
ATOM    906  N   ILE A 134     -28.335  20.013  15.849  1.00 65.16
 -0.171 NA


The version string of prepare_receptor4.py: v 1.13 2010/01/25 23:37:14

For now, I am using obabel to first convert to pdbqt and then having
prepare_receptor4.py reprocess the resulting file.

Aaron
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