VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Sep 16 2005 - 18:22:43 CDT

There was discussion on this topic last fall. Check out
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3237.html

and see if this answers your questions.

Regards
Brian

On Fri, 16 Sep 2005, Kara Di Giorgio wrote:

> I need to calculate RMSDs for a series of trajectories compared to a
> "base" structure. I have trajectories for the "base" structure and all
> of my other molecules. I've played around with the RMSD function in
> VMD (and downloaded the advanced plugin), but I need to generate an
> average structure of the last 50 steps of my "base" trajectory and save
> it as a pdb to use it as the reference. Has anyone created a script to
> do this? I generated my trajectories in Amber.
>
> Thank you for any help,
>
> Kara Di Giorgio
> University of the Pacific
> Stockton, CA
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
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