From: Raluca Mihaela ANDREI (r.andrei_at_sns.it)
Date: Thu Sep 18 2008 - 07:33:00 CDT

Thanks a lot! I managed to visualize the electrostatic
potential but I would like to do it in an automatic way,
because I need to calculate the electrostatic potential and
then save as .wrl file in order to import it into a 3D
software. This must be done in every frame of an animation. Is
it possible to do all these from the command line of Windows?
Thanks,
Raluca

On Tue, 16 Sep 2008 11:01:18 -0500
  John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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