VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 13 2007 - 14:32:22 CDT

Per,
  Where did you need to set the working directory in order to
cure the problem, was that done in the APBS plugin "settings" menu?
The default working directory should have been /usr/tmp, does your
linux system not have a /usr/tmp directory? Clearly some sort of
warning ought to be generated if there's a problem with the working
directory, though I'll need to be able to reproduced your particular
problem in order to track it down and fix it.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 13, 2007 at 08:08:29PM +0100, Per Jr. Greisen wrote:
> Hi,
>
> Sorry for the short description. First I tried on different proteins but I
> get the same problems with the tutorial on APBS with the 1MYK.pdb
> (http://apbs.sourceforge.net/doc/tutorial/#vmd-sect).
>
> My VMD is 1.8.5 and the APBS is 0.4.0 and my OS is UBUNTU. So I start by
> converting the 1MYK.pdb into the 1MYK.pqr on the internet server - this
> works fine. I select the diffult parameters for the conversion(so I think
> it is AMBER force field that is used). I load the molecule(1MYK.pqr) with
> VMD and go the APBS. I check the setting that the apbs (execution file is
> in the coorect path) and I press okay. Than I select the 0 and press
> "edit" and press okay to the default values suggested by the menu.
> The terminal window says "Status: ready" - so I press "Run APBS" and now
> it works!
>
> So the problem was that in case - I need to set the usr/tmp to the working
> directory otherwise it will not work. BUT it didnt give any errors in my
> case fx. wrong directory. Sorry for disturbing you.
>
>
>
> > Hi,
> > What version of APBS are you running, and on what platform?
> > The APBS plugin included in VMD 1.8.5 should work fine with APBS 0.4.
> > Your description of the problem doesn't include any details on what you
> > mean by "the program starts to crash", are you talking about APBS? If so,
> > what do you mean by "it starts to crash"? Does it emit warnings or errors
> > of some kind, if so, please send them, as this short description is so
> > vague
> > can't really say much without additional information. You didn't say what
> > kind of APBS calculation you ran either, it would be very helpful to know
> > what you actually did. The APBS plugin has worked fine for us here, but
> > you may be trying something unusual that triggers a bug, or you may be
> > using a different version of ABPS which behaves differently. Additional
> > information would be helpful.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Mar 13, 2007 at 07:32:04PM +0100, Per Jr. Greisen wrote:
> >> Hi,
> >>
> >> I am running the APBS analysis as an extension from the VMD menu but it
> >> seems that something goes wrong.
> >>
> >> I start by generating the *.pqr file from the webserver as prescribed
> >> from
> >> the tutorial. I load the *.pqr file into vmd and go to the APBS, select
> >> the molecule, edit in order to see if the default parameters are okay -
> >> than I press "RUN APBS" and than the program starts to crash. The
> >> vmd-console displays apbsrun) Running job mode=normal and if I go into
> >> the
> >> "top" I see that vmd is running - I never see apbs executed which I find
> >> rather strange.
> >> And than it just keeps on running until I kill the job. If I execute the
> >> abps outside of VMD it takes no time to do the calculations.
> >>
> >> How to fix so it can be executed within VMD. Any help or advices
> >> appreciated. Thanks in advance
> >>
> >> Best Regards
> >>
> >> Per
> >
> > --
> > 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
> >
>
>
> --
> Best Regards
>
> Per Jr. Greisen
> 

-- 
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