Re: [AMBER] RMS2D maybe?

From: Daniel Roe <>
Date: Mon, 18 Nov 2013 08:33:58 -0700


On Sun, Nov 17, 2013 at 12:06 PM, Fabrício Bracht <> wrote:
> Hi, I have a protein which is a homo-dimer, i.e., subunit A is identical in
> sequence to subunit B. I would like to know how each structure evolve
> relative to the other one during md. Actually I only want to analyze 8
> residues from the active site. The manual states that rms2d calculates the
> rms of each frame to each other frame. That means that I'll have a
> comparison between frame 1 and all the other frames individually, frame 2
> and all the others....etc, right?


> But does that mean that I can calculate
> the rms of frame 1 for Residues 1,2,3 using as reference residues A,B,C for
> all the other frames. Is this the proper way to do this type of analysis?
> I've tried:
> rms2d Sitio :202,204,206,257,259,260,261,264.C,CA,N rmsout rmsd-sitio.gnu refttraj mdcrd.md2 :31,33,35,86,88,89,90,93.C,CA,N

This is calculating the rmsd of atoms in the first mask from your
input trajectories to atoms in the second mask from trajectory
mdcrd.md2, which is I think what you want. Let me know if you have any
more questions.

Hope this helps,


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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Nov 18 2013 - 08:00:03 PST
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