VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 05 2001 - 12:49:10 CDT

Hi,
  Just got back into town, was giving a talk about VMD at a CAVE and VR
workshop: http://www.pdc.kth.se/projects/vr-cube/workshop.html

On the PDB loading problem: If VMD hangs loading your PDB file, there
must be some misplaced or missing data in the file. I can send an example
of a multiple-frame PDB file if you like, or you could use Babel to produce
one for yourself. We'll probably be improving our support for some of these
variants of the PDB format soon.

I saw that you've already figured out how to load the PDB + CRD using
the edit menu, so let us know if you run into any other snags.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 04, 2001 at 10:44:41AM -0400, tom keyes wrote:
> On Thu, Oct 4, 2001 1:47 AM, B. Bennion <mailto:bbennion_at_u.washington.edu>
> wrote:
> >crd files work very nicely. This file is just a text file with three
> >columns of atomic positions, VMD does need to know how many atoms to put
> >in a single frame though. My group used crd files for awhile. An
> >intitial pdb file will give cmd what it needs to know.
> >
> >your can access several file formats using the molecule menu.
>
> Brian,
> Thanks, it would be very convenient to be able to use a text file with 3
> cols xyz, my usual way of writing trajectories. However all I find in the
> Molecule menu using crd is parm and crd. How do you load pdb and crd? If I
> figure out how to write a parm file can I just load it plus my trajectories
> renamed .crd?
> BTW I said yesterday VMD choked on loading a big file of repeated pdb
> files for different time steps. When I made the file smaller by taking just
> a few time steps it read it but said it was one frame with more atom, the
> number of atome = the true number times the number of time steps.
> Tom
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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