Hi,
I've heard this from a few people, and the answer seems to be that the new
version of APBS doesn't like chain information in the PyMOL-generated PQR
files. I'll release a new version of the plugin that fixes this soon, but
in the meantime, the easy solution is to remove the chain information from
the PDB file before you start the APBS calculation.
There are a couple of other errors in your run:
- APBS is complaining that I'm using an old style of input file. I'll
fix that in the next version of my plugin, but the old style still works,
so it's not really causing trouble.
- PyMOL couldn't assign charges/radii to some of your atoms. Do you have
a non-standard protein residue? If not, it may be that you have a
terminal residue that PyMOL/champ doesn't understand. Can you look at the
PQR file to see which residues ended up with radii and charges of 0?
thanks,
-michael
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Mon, 22 Nov 2004, Peter Haebel wrote:
Hi Michael,
i have just updated to the latest version of apbs-0.3.2 and pymol-0.97 under
debian linux and get the following error messages (see below) + a completely
positively charged protein surface...
using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html' of the
same protein works, so there seems to be a problem with the build-in
generation of pqr-files.
i tried 3 different proteins from the PDB with and w/o ligand and water atoms.
any idea what's going wrong?
cheers,
Peter
------------------------------------------------------------------------------
PDB code 1ini
all waters and ligand atoms removed by hand
...
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated
Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated
Hydrogens and termini so i am returning pymol-generated.pqr
WARNING: 5 atoms did not have formal charges assigned
WARNING: 10 atoms did not have properties assigned
...
This executable compiled on Nov 22 2004 at 15:59:46
Parsing input file pymol-generated.in...
parsePBE: Warning -- parsed deprecated "bcfl 1" statement
parsePBE: Please use "bcfl sdh" instead.
NOsh: Warning -- parsed deprecated statment "chgm 1".
NOsh: Please use "chgm spl2" instead!
parsePBE: Warning -- parsed deprecated "srfm 1" statement.
parsePBE: Please use "srfm smol" instead.
parsePBE: Warning -- parsed deprecated "calcenergy 0" statement.
parsePBE: Please use "calcenergy no" instead.
parsePBE: Warning -- parsed deprecated "calcforce 0" statement.
parsePBE: Please use "calcforce no" instead.
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
Valist_readPDB: Unable to parse resSeq token (A) as int!
Valist_readPDB: Error while parsing residue name!
Valist_readPQR: Error parsing ATOM field!
Error while reading molecule from pymol-generated.pqr
Error reading molecules!
ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
DXStrToMap: Dimensions: 129 129 97
DXStrToMap: Origin 14.554 -48.010 -7.484
DXStrToMap: Grid 0.579 0.523 0.664
DXStrToMap: 1614177 data points.
ObjectMap: Map Read. Range = 3352.843994 to 12333.959961
___________________________________________
Peter Haebel
Philipps-Universität Marburg
Institut für Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg
phone: +49-6421-28-25072
fax: +49-6421-28-28994
email: peter.hae...@staff.uni-marburg.de
http://www.agklebe.de
NAD3-Workshop 2005 - Divide&Conquer
http://www.agklebe.de/workshop2005
