Hello --

Could you please attach the PyMOL-generated APBS input file as well?



On Tue, Dec 23, 2008 at 4:46 PM, Roland Schmucki <roland.schmucki@gmail.com> wrote:
Hello !

I am using PyMol on a computer with Windows Vista.

I have prepared a pdb- and pqr-file (attached). Now, I'd like to make
the potential surface plot by using the APBS plugin in PyMol. I have
downloaded the APBS binary and specified the correct path in the PyMol
APBS Tools menu. In addition, I have set the option (Main options in
PyMol APBS Tools) so that my own pqr file is used.

Now, after "Set grid" and "Run APBS" the following error message
appears in the console:

APBS Tools: set pqr file to C:\Users\Roland\Desktop\polyB-Hamada\polyB-Opalp.pqr
cs [4, 2, 2]
finedim [63.161001205444336, 30.231099987030028, 30.479299831390382]
nlev 4
mult_fac 32
finegridpoints [129, 65, 65]
 APBS Tools: coarse grid: (73.374,30.231,30.479)
 APBS Tools: fine grid: (63.161,30.231,30.479)
 APBS Tools: center: (2.391,0.702,0.251)
 APBS Tools: fine grid points (129,65,65)
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?

I have searched the archives of the mailing lists for PyMol, APBS, and
also the "Troubleshooting" section at the bottom of this page:
http://www.pymolwiki.org/index.php/APBS but could not find a solution

I would appreciate any suggestion and help.

Thank you very much.

Roland Schmucki
PhD student
Institute of Biophysical Chemistry
Goethe-University Frankfut am Main, Germany


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Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/