VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2005 - 15:38:06 CDT

Hi,
  Take a look at the trajectory_smooth script here, it should do what you want
with a little coaxing:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_smooth/

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 16, 2005 at 11:01:34AM -0700, 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 

-- 
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
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