Re: AMBER: RMSD Calculations

From: <>
Date: Mon, 05 Dec 2005 11:29:23 -0500

Hi Kara,
        I have tackled a similar problem as yours. Andrew Martin has
developed a nice little program called ProFit that will perform an
RMSd fit to specific residue of PDBs that contain different number of
atoms. You can use this program (a very short learning curve) to
compare your DNA base pairs with and without the ligand. The program
can be downloaded from Martin's website at

Hope this helps,
Karl N. Kirschner, Ph.D.
Visiting Assistant Professor of Chemistry
Hamilton College, Clinton NY 13323

On Dec 5, 2005, at 10:22 AM, Kara Di Giorgio wrote:
> I was wondering if anyone could help me learn how to calculate the
> RMSDs of my trajectories. I have used ptraj in the context of the
> Amber tutorials, but I'd like to do something slightly different
> and don't know how to go about doing it

> I have a MD simulation of a piece of DNA with a compound in it. I
> also have a MD simulation of the DNA without the compound. I'd
> like to look at how the DNA differs.
> This is what I was thinking of:
> 1. I am going to get an average structure of the DNA for the last
> 50 ps (where it is stable) and save it as a pdb. (I have a
> smoothing script for VMD to do this.)
> 2. I would like to compare the backbone of the DNA in my
> trajectory to the backbone of the averaged DNA-only pdb.
> 3. I would also like to compare the base-pairs of the DNA in my
> trajectory to the base-pairs of the averaged DNA-only pdb.

> I'm also worried that it will only calculate the RMSD if there are
> an identical number of atoms in each, which I don't have.
> My trajectories are in multiple parts (_md1.mdcrd, _md2.mdcrd, etc)
> so that if my computer bombed, I wouldn't loose an entire day's
> calculations.
> Does anyone have any suggestions? Either using ptraj or another
> program? If it's with ptraj, a sample input line would be helpful
> to clarify the input syntax needed.
> Thank you,
> Kara Di Giorgio
> University of the Pacific
> Stockton, CA
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Dec 05 2005 - 17:53:00 PST
Custom Search