Re: [AMBER] Backbone Rmsd

From: David A Case <>
Date: Tue, 17 Mar 2015 07:52:50 -0400

On Mon, Mar 16, 2015, jacob wick wrote:
> rms first out rna_run.rms .P,O3',O5',C3',C4',C5' time 0.50
> Is this script helping in comparing backbone of reference with the backbone
> of frames (without taking residues deviations in account) or it is
> superimposing the reference backbone with the backbones of frame and giving
> the deviations with respect to the residues?

The former. A command like this superimposes frames on the backbone atom,
and reports the RMS value computed over the same set of atoms.

If you want to fit on one set of atoms, but calculate the deviations for a
second set of atoms, you need two rms commands. The first is like that above,
which will do the superposition. The second one would have a different atom
mask, and the keyword "nofit", so that no additional fitting would be

Play with this a bit on some very simple system to see what is going on.


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Received on Tue Mar 17 2015 - 05:00:04 PDT
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