Re: script for calculation of an rmsd

From: Branko (
Date: Sat Oct 30 2010 - 07:09:44 CDT


You have built-in RMSD calculation tool in VMD, under analysis. Only
select atoms that you want for your molecule (antibiotic). Also you
should browse VMD user guide, particularly

The second option is to use VegaZZ - also free as well as VMD and NAMD
there you find comfortable user interface for (really) widespread types
of trajectory analysis.



On 10/30/2010 10:41 AM, wrote:
> Hi, I want to calculate the rmsd of an antibiotic with a script, but I have
> script only for proteins. Could anyone tell me where I can find. Also, I want
> to learn how to write script. I must read tutorials of tcl only or something
> especially for namd?
> Thank you in advance.
> Maria
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