VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 20 2006 - 20:57:38 CST

Hi,
  You can read these PDB files into VMD and then write out a new
trajectory file from them. I'm assuming that all of your PDB files
contain the same number of atoms, yes? If so, you can use a script
like this one to load the sequence of PDB files into VMD:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/

>From that point, you can save them back out in a new trajectory
file using the File->Save Coordinates menu item in the
VMD Main window.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 20, 2006 at 05:14:22PM -0600, Narender Singh Maan wrote:
> Dear All,
> I have 30 pdb files that i have extracted from a trajectory from my
> simulation. My question is, is there any way to make a new trajectory file
> (dcd or xtc) from just these 30 frames? I tried using catdcd, but its not
> able to read pdb files ("error:failure opening x1.pdb, returned -6"). Any
> suggestions would be of great help.
> thank you
> singh 

-- 
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