Re: rmsd

From: Chris Harrison (
Date: Mon Nov 01 2010 - 13:23:36 CDT

Dear Divya,

For the best possible answer, you should post this question to the VMD list
( ).


On Mon, Nov 1, 2010 at 3:30 AM, divya nayar <>wrote:

> Hi
> I want to calculate RMSD of solvated peptide using Tcl script in VMD. I
> want to find RMSD with respect to a reference structure i.e.minimized
> crystallographic structure and not frame 0 of the trajectory (as mentioned
> in rmsd.tcl given in tutorials). How can I use another molecule (minimized
> crystallographic structure) in the same script to mention reference
> structure appropriately in the 'atomselect' option?
> Thanks,
> Divya

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078

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