From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Nov 01 2010 - 13:23:36 CDT
For the best possible answer, you should post this question to the VMD list
( http://www.ks.uiuc.edu/Research/vmd/mailing_list/ ).
On Mon, Nov 1, 2010 at 3:30 AM, divya nayar <divya.alchemist_at_gmail.com>wrote:
> 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?
-- 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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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