VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 03 2005 - 15:27:01 CST

Leyla,
  When you attempt to load the Charmm CRD file into VMD, you'll need
to manually specify the plugin type to VMD by selecting "COR" type
from the list of plugins. Unfortunately, both Charmm and AMBER use
"CRD" for various things and VMD doesn't presently have a way to guess
which one it actually is, so you need to help it by manually specifying
the plugin to use when you load it. Let us know if you still need help.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 01, 2005 at 11:35:27AM +0100, Leyla Celik wrote:
>
> Hello again,
>
> As it is, I have a couple of old crd files that I have been trying to read into
> VMD, but instead of opening the file I just get a
>
> "Problem reading CRD file"
>
> I have tried to open corresponding psf and crd files to, but none of the options
> works...
>
> Any suggestions?
>
> Leyla
>
>
>
> Citat John Stone <johns_at_ks.uiuc.edu>:
> >
> > Leyla,
> > At the present time the VMD plugin for CHARMM 'crd' coordinate
> > files can only read them, it doesn't have the ability to write new files.
> > Someone with expertise in the CHARMM coordinate file format could probably
> > add the export/write capability to the VMD plugin in a few hours.
> > I'd be happy to help someone do this if someone with the expertise and
> > ability to verify/test the results wants to work on it.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Thu, Feb 24, 2005 at 08:31:03PM +0100, Leyla Celik wrote:
> > > Hello,
> > >
> > > I am tryin to use CHARMM to analyse my NAMD simulation output but need a
> > CHARMM
> > > crd and psf file as inputs besides the dcd. I figured out how to write a
> > CHARMM
> > > psf file in VMD/psfgen but I haven't been able to create the relevant crd
> > file.
> > > Is it possible using VMD? Or does anyone have another solution?
> > >
> > > Thanks
> > > Leyla
> > >
> > >
> > >
> > > --
> > > Leyla Celik
> > > Ph.d. student
> > > Department of Chemistry
> > > University of Aarhus
> > > Langelandsgade 140
> > > DK-8000 Aarhus C
> > > Denmark
> > > Tel: +45 8942 3869
> > > e-mail: lc_at_chem.au.dk
> >
> > --
> > 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
> >
>
>
> --
> Leyla Celik
> Kemisk Institut
> Aarhus Universitet
> Langelandsgade 140
> 8000 Århus C
> Danmark
> Tlf: +45 8942 3869
> e-mail: lc_at_chem.au.dk 

-- 
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