VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 02 2011 - 09:44:03 CDT

Hi,
  Did the path to your working directory contain spaces?
I know that spaces in filenames caused problems with APBS
in the past, perhaps that's what is going on here. What happens
if you change to a directory that contains no spaces and do the
calculations there?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 02, 2011 at 11:00:50AM +0100, Asmaa Elsheshiny wrote:
> Hi,
> Sorry about the delayed replay. I have done the following
> * check that apbs running.
> *check the apbs working directory
> * ran a test apbs with vmd on a smaller molecule.
> I found that the calculations were done and i can follow it through vmd console, but at the final step where *.dx file is created, vmd cannot read the output and then stalled.
> I have followed the apbs with VMD online tutorial step by step. So what is the cause of this error? any help is greatly appreciated.
> Best Regards,
> asmaa
>
> _______________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Tuesday, May 10, 2011 9:09 PM
> To: Asmaa Elsheshiny
> Cc: VMD
> Subject: Re: vmd-l: apbs with vmd, no output
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078