VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 27 2011 - 14:43:04 CDT

Ricardo,
  To check APBS in the system console, just type "apbs" and see if you
get the normal ABPS run messages, or if it gets a segmentation fault or
anything like that. If it works, then this may be an issue with changes
in the APBS input file format in the version you're using. Can you tell
me what kind of calculation you setup in VMD in more detail? If APBS runs
when you try running it on the command line, then I'll want you to send
me a copy of the APBS input config file that the VMD plugin generated.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 24, 2011 at 04:39:56PM -0200, Ricardo Oliveira dos Santos Soares wrote:
> Hello Mr. Stone,
>
> I believe it ran, because apbs works fine with PyMol. How can I run apbs in
> the linux console, so I can make sure it is working properly?
>
> Thanks for your help.
>
> Ricardo.
>
>
>
> On Mon, 23 May 2011 15:12:51 -0500, John Stone wrote
> > Hi,
> > Did APBS actually run? Usually when this happens it is because
> > the apbs binary didn't run successfully. Have you run APBS by hand
> > at least once to verify that it works?
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, May 23, 2011 at 05:55:00PM -0200, Ricardo Oliveira dos
> > Santos Soares wrote:
> > > Dear users,
> > >
> > > I'm using VMD 1.9 and there's an issue when using APBS plugin. The console
> > > states:
> > >
> > > Cannot access output file /usr/tmp/apbs.79178/pot.dx
> > >
> > > But in that directory, there's a file called pot-PE0.dx
> > >
> > > Has anyone had this problem before?
> > >
> > > Thanks in advance.
> > >
> > > Ricardo.
> > >
> >
> > --
> > 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
>
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-- 
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