VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 20 2006 - 22:46:26 CST

Jennie,
  I'll have to take a look at the AMBER CRD plugin tomorrow and see if the
problem is simply that it doesn't include code to write the box
information. If so, it may be a simple matter to add and send you a
new version of the AMBER CRD plugin to try out.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 20, 2006 at 08:09:12PM -0800, Jennie Thomas wrote:
> Hi VMD experts,
>
> I have an analysis code (separate from VMD) that reads in AMBER
> coordinate files. Someone has asked if I can use this code to
> analyze a dcd trajectory, so I decided to try and use vmd to convert
> from dcd to crdbox format. However, the box information is not
> preserved when doing this. Because this is a constant pressure
> simulation I need to use the box information at every step. Do you
> know how to force vmd to write box information?
>
> I have a simple tcl script I am using:
>
> # Load the system and the trajectory
> mol new "box.cor" type cor
>
> mol addfile "00.trj" type dcd waitfor all
> mol addfile "01.trj" type dcd waitfor all
>
> animate write crdbox traj.crd
>
> Do I need to be doing something more complicated to get box
> information? Or does anyone have another suggestion for a file
> format conversion tool?
>
> Thanks,
> Jennie Thomas 

-- 
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