VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 18 2007 - 16:59:19 CDT

Moumita,
  I should also note that it appeared that you were running a very old
version of VMD (VMD 1.8.3!!), if you intend to work with CMAP, you
should be running VMD 1.8.6, which has the latest revs of psfgen.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 18, 2007 at 04:47:25PM -0500, John Stone wrote:
> 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 

-- 
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