VMD-L Mailing List

From: Matthias Negri (thias_at_scfarm.unibo.it)
Date: Tue Aug 30 2005 - 06:53:28 CDT

Hi,
thanks a lot for the hint with crdbox.
I solved my problems now, with a great movie!!! .. it was really a small
problem! with an easy solution!!
But why is the crd plugin not recognising even gunzipped crd-files.. is
there an upgrade to expect or have I each time to unzip my crd-files??

Thanksfulle, Matthias Negri
>
> 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
>
>