VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 21 2005 - 14:59:51 CST

Hi,
  If you've been running NAMD simulations, you'd normally have
DCD format trajectory files as output rather than just PDB files.
Is there some reason you're loading PDBs rather than DCD files?
If necessary, you can indeed load a large number of PDB files in
VMD with a simple script:

proc loadpdbtraj { filespec } {
  foreach pdb [glob $filespec] {
    mol addfile $filespec
  }
}

To use it, do this:
  loadpdbtraj /my/files/*.pdb

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 21, 2005 at 01:43:48PM -0500, Jindal Shah wrote:
> Hello,
>
> I am trying to generate a movie from an NAMD simulation. I was wondering
> if I can load all the pdb files at once and then create a movie. I am
> running
> VMD on windows machine.
>
> Another option, I thought of combining all the pdb files into one file and
> then
> loading into VMD. However, when I do that, total number of atoms corresponds
> to the number of lines in my combined pdb file and I only get 1 frame? Am I
> losing
> any information while combining files? do I need to add anything to suggest
> that it is a trajectory file?
>
> Thanks
> Jindal 

-- 
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