AMBER: RMSD Calculations

From: Kara Di Giorgio <>
Date: Mon, 5 Dec 2005 07:22:03 -0800

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 not very familiar with ptraj and I'm sure I don't have the syntax
correct. I've never gotten it to work with comparing to a separate pdb
file, only comparing to the starting structure.

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

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

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Received on Mon Dec 05 2005 - 15:53:00 PST
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