VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 18 2007 - 16:47:26 CDT

Hi,
  I read the output of psfgen that you provided, it just verifies
that psfgen doesn't like the format of the topology files you're
reading in. In particular, it doesn't recognize the formatting of the
CMAP entries. Can you post a copy of the topology file(s) you're
working with?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 13, 2007 at 09:05:25AM +0000, Moumita Maiti wrote:
> Hi,
>
> I have deposited the output of fsfgen into the VMD biofs area and
> name of file is psfgen_output.
>
> Regards,
> moumita
>
> On 6/13/07, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Hi,
> > Can you actually send the text of the error message you're
> >getting from psfgen? I will have to check with the authors of
> >psfgen etc to determine what's going on there. If you can provide
> >us with a copy of the files and the error messages you're getting
> >that would be very helpful. Don't mail the files to the VMD-L mailing
> >list, either post them on the web or deposit them into the VMD
> >biofs area on biocore, see:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Mon, Jun 11, 2007 at 05:52:23AM +0000, Moumita Maiti wrote:
> >> Hi,
> >>
> >> We had installed vmd source file in AMD opteron system and
> >> pentium clusters. vmd works fine for pentium machine.
> >>
> >> But vmd can not load a molecule in AMD opteron system which has redhat
> >> operating system(OS) if the cluster is logged in from mandrake operating
> >> system. It works if we login from fedora/redhat OS.
> >>
> >> Running psfgen pgn file with vmd in AMD system gives CMAP error in any
> >OS,
> >> whereas same input pgn file and topology file does not give any CMAP
> >error
> >> in pentium cluster.
> >>
> >> What can be the possible problems?
> >>
> >> Regards,
> >> moumita
> >
> >--
> >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
> > 

-- 
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