Re: [AMBER] rmsd calculation

From: David A. Case <>
Date: Tue, 7 Jun 2011 07:32:26 -0400

On Tue, Jun 07, 2011, Xiao Chen wrote:
> How can we calculate
> a)rmsd of each residue (backbone) at each frame in the simulation (not
> r.m.s.f).

You first do an ordinary rms fit on whatever atoms (say all the backbone) that
will remove overall translation and rotation.

Next, you do an rms fit with the "nofit" keyword, say on a certain residue,
which will calculate the rmsd from the reference structure just for the atoms
in the current mask.


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Received on Tue Jun 07 2011 - 05:00:03 PDT
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