VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Tue Nov 02 2010 - 13:01:09 CDT

Take a look into the User's Guide, section 11.4.2.
You should also make yourself familiar with the atomselect command.

As a start:
say, mol 0 is a crystal structure,
mol 1 is a trajectory, and
you want to measure rmsd between the crystal and and step 100 of the
trajectory for the backbone of residues 25 to 35

set a [atomselect 0 "residue 25 to 35 and backbone"]
set b [atomselect 1 "residue 25 to 35 and backbone" frame 99]
measure rmsd $a $b

#free memory
$a delete
$b delete

eddi

On Tue, Nov 2, 2010 at 11:53 AM, divya nayar <divya.alchemist_at_gmail.com> 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?
>
> Also, when a selection of "backbone" of peptide is made in atomeselect, does
> it include havy atoms from the side chains as well?
>
> Thanks,
> Divya Nayar
>
>
> 

-- 
--
=============================================================================
Eduard Schreiner
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
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
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