VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 30 2005 - 10:15:22 CDT

Hi,
  VMD doesn't recognize any compressed (gzip, zip, bz2, etc) file formats
presently, though this is something I plan to support in a future version.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 30, 2005 at 01:53:28PM +0200, Matthias Negri wrote:
> 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
> >
> >
> 

-- 
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