VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 01 2006 - 14:10:18 CDT

Hi,
  The 'mol load' syntax is on it's way out... You'll want to use the
new 'mol new'/'mol addfile' commands instead:
  mol new my_system.psf
  mol addfile my_system.dcd

For your specific question, you can do this:
  mol new my_system.top type parm7
  mol addfile my_system.dcd

If your parm file is named .prmtop the new version of VMD will recognize
it as an Amber 7/8/9 toplogy file automatically.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 01, 2006 at 08:43:12PM +0200, L. Michel Espinoza-Fonseca wrote:
> Hi all,
>
> I have a simple question --it's better to ask than do something stupid
> ;)--. I have a trajectory in dcd format created by namd and the amber
> 7 topology file of my system. Usually, when I load my molecules on
> VMD, I use the following command:
>
> mol load psf my_system.psf dcd my_system.dcd
>
> I was wondering if I can do something similar with my topology (let's
> say, changing "psf my_system.psf" by "amber my_system.top")
>
> Thanks!
> Michel 

-- 
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