Hi,
(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.
-Dan
On Wed, Nov 23, 2016 at 5:07 AM, Sepideh Jafari
<sepidejafari71.gmail.com> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Nov 23 2016 - 05:30:03 PST
