VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 05 2005 - 17:17:10 CDT

This could probably be done by modifying Luis Gracia's RMSDTT
plugin a bit. You'd need to do the plotting part with your
own scripts and/or additional software. There's also a
per-residue RMSD script included in one of the VMD/NAMD
tutorials that you might be able to adapt for this purpose.
  http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node12.html

  John

On Tue, Apr 05, 2005 at 09:24:28AM -0700, Anuradha Mittal wrote:
> Hi!
> I need the script to get the rmsd of each residue for the entire
> trajectory. The available scripts either calulates the average rmsd of
> each residue for the whole trajectory or average rmsd of the whole
> protein for the entire trajectory.In a way i want a combination of
> both scripts. I require to plot a 3d graph with three axis as residue
> number,rmsd and time step.
> does anyone has the script to get this data?
> Thanks
> Anu 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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