VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 29 2005 - 09:43:30 CDT
- Next message: Bob Johnson: "Error in visualizing the 5 prime end of DNA strand"
- Previous message: Matthias Negri: "Problems with AMBER trajectories (MOVIE!) and crd-files"
- In reply to: Matthias Negri: "Problems with AMBER trajectories (MOVIE!) and crd-files"
- Next in thread: Matthias Negri: "Re: Problems with AMBER trajectories (MOVIE!) and crd-files"
- Maybe reply: Matthias Negri: "Re: Problems with AMBER trajectories (MOVIE!) and crd-files"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Bob Johnson: "Error in visualizing the 5 prime end of DNA strand"
- Previous message: Matthias Negri: "Problems with AMBER trajectories (MOVIE!) and crd-files"
- In reply to: Matthias Negri: "Problems with AMBER trajectories (MOVIE!) and crd-files"
- Next in thread: Matthias Negri: "Re: Problems with AMBER trajectories (MOVIE!) and crd-files"
- Maybe reply: Matthias Negri: "Re: Problems with AMBER trajectories (MOVIE!) and crd-files"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]