VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 16 2008 - 11:01:18 CDT
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Hi,
What working directory did you use? It turns out that there are some
issues with APBS and filenames that contain spaces. The new versions of
APBS have fixed these problems, and we are in the process of updating the
APBS plugin for VMD similarly, but in the mean time you will likely need
to make a working directory path that contains no spaces, e.g. c:/apbsrun
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Tue, Sep 16, 2008 at 10:28:02AM +0200, Raluca Mihaela ANDREI wrote:
>
> Hi,
> I would like to visualize in VMD the electrostatic potential
> of a protein. I am following this tutorial:
> http://apbs.sourceforge.net/doc/tutorial/#vmd-sect
> I am working in Windows, I downloaded apbs-1.0.0. I imported
> the pqr file into VMD (1.8.6), then in APBS tool I wrote the
> paths for Working Directory and APBS Location, I ran APBS and
> I receive the following message error: "APBSRun:output file
> missing or unreadable". In the folder for Working Directory a
> .pqr and an .in files are created.
> Can somebody tell me what am I doing wrong?
>
> thanks!
> Raluca
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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