Re: [AMBER] RMSD calculation of a homodimer

From: Daniel Roe <>
Date: Sun, 4 Jan 2015 17:32:12 -0700


On Sun, Jan 4, 2015 at 9:21 AM, Ibrahim Said <> wrote:
> Dear Amber users
> I ran a Molecular Dynamics simulation for 10ns. My protein is a homodimer
> composed of two subunits. The two subunits are with different residue
> lengths (x-ray file). Please, can I find a hand to write script
> for calculating the RMSD of the two subunits individually. My Amber is
> version 12.

First, I recommend upgrading to AmberTools 14 for analysis (freely
available here:

To calculate the RMSD of a single subunit to the first frame using
cpptraj, use something like the following input:

parm myparm.parm7
rms first <mask> out rmsd.agr

where <mask> is an Amber atom mask expression that describes the
subunit of interest (e.g. :1-130 for residues 1 to 130, etc).

See the cpptraj section of the Amber14 manual for more on atom masks
and the rmsd command. Also check out tutorial C1, which explicitly
covers RMSD calculation with cpptraj


> thank you in advance,
> said
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Jan 04 2015 - 17:00:02 PST
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