VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 29 2005 - 09:43:30 CDT

Hi,
  If your trajectory was produced from a simulation with periodic boundary
conditions, you will need to load it as a "crdbox". Try that end let us
know if you still have trouble.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Aug 29, 2005 at 11:19:19AM +0200, Matthias Negri wrote:
>
> Hello, I have some problems while visualizing AMBER trajectories and
> making movies from AMBER crd-files!
> I'm working on a protein/DNA complex.
> If I convert the crd-file in a pdb, the complex looks good, with
> acceptable geometrical values, according to ptraj and Procheck. But if I
> watch the crd file in VMD, the complex results distorted, specially one
> DNA helix is changed in size,form AND position!! (and that even if it
> doesn't result in the pdb. What's the reason for?
> I nedd to create a good trajectory movie, but it seems harder as I
> thought! Is it because of the DNA?
>
> Any help or hint would be appreceated, thanks in advance
>
> Matthias Negri
> thias_at_scfarm.unibo.it 

-- 
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