VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 10 2011 - 15:09:39 CDT

Hi,
  Can you verify that you're able to run APBS manually?
Most of the times problems like this have arisen previously, they
were caused by ABPS binaries that didn't run correctly (and had never
been tested outside of using the VMD plugin). If you are able
to run the APBS binaries outside of VMD, then I'll need to get
a little more information from you so I can try and reproduce your
problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 10, 2011 at 06:14:08PM +0100, Asmaa Elsheshiny wrote:
> Dear all,
> I tried to use apbs 1.2.1 version with vmd 1.8.7. It sounds working but no output has appeared in the working directory, and the most important thing is the program was still working even when i use smaller peptide to test it. so, what do suggest?
> Note, nothing wrong in the PQR file I have generated it by pdb2pqr web server. and I have used the online tutorial provided by apbs to be used by vmd for the electrostatic potential visualization step by step.
> Cheers,
> asmaa 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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