VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 18 2006 - 12:37:27 CDT

Hi,
  Is it actually a trajectory (CRD) file, or is it a restart file?
They are slightly different, and mistaking one for the other can
cause this problem. If it's a restart file, you'll want to use
the rst7 plugin to load it.

  John

On Tue, Jul 18, 2006 at 09:32:37AM -0400, campen_at_geosc.psu.edu wrote:
> Dear all:
>
> I've been trying to use the builder and Amber parameter set available for
> carbohydrates from Robert Woods group (www.glycam.com) and visualize these
> structures in VMD (in preparation for simulating them in NAMD).
>
> I've found that I can generally produce a structure for a small test case
> (if I read in first the PARM information and then the .crd file) but most
> of the geoemtric parameters are screwed up (e.g. one atom is about 30
> angstroms away from the others).
>
> Any suggestions as to how to solve this issue would be greatly appreciated.
>
>
> Kramer Campen
>
> 

-- 
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