[PyMOL] APBS plugin - warnings generating pqr files

Hi Michael,

i have just updated to the latest version of apbs-0.3.2 and pymol-0.97 unde=
r=20
debian linux and get the following error messages (see below) + a completel=
y=20
positively charged protein surface...

using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html' of =
the=20
same protein works, so there seems to be a problem with the build-in=20
generation of pqr-files.

i tried 3 different proteins from the PDB with and w/o ligand and water ato=
ms.

any idea what's going wrong?=20

cheers,

Peter

=2D------------------------------------------------------------------------=
=2D----

PDB code 1ini
all waters and ligand atoms removed by hand

=2E..
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated=
=20
Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated=
=20
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
=2E..

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 =3D 3352.843994 to 12333.959961

 ___________________________________________

Peter Haebel

Philipps-Universit=E4t Marburg
Institut f=FCr Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg

phone: +49-6421-28-25072
fax: +49-6421-28-28994

email: pet...@st...
http://www.agklebe.de

NAD3-Workshop 2005 - Divide&Conquer
http://www.agklebe.de/workshop2005