Re: [AMBER] rmsf problem

From: Daniel Roe <>
Date: Wed, 23 Nov 2016 08:06:31 -0500


(In the future it would be better to at least provide the cpptraj
input you used so we have more information.)

I suspect you may not have removed global rotational/translational
motion from your structure (via fitting) prior to the rmsf/atomicfluct
command. If not, you should add an 'rms' command prior. See section
29.9.4 in the Amber 16 manual for full details.


On Wed, Nov 23, 2016 at 5:07 AM, Sepideh Jafari
<> wrote:
> Dear amber users
> I performed some MD run for ERK protein and analyzed it with RMSF test
> But i have problem with it, because the values of the the graph of rmsf are
> not normal.
> I there anyone help me with this?
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Wed Nov 23 2016 - 05:30:03 PST
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