Hi,
I suspect you haven't removed global translations/rotations from your
system. Try doing an rms-fit to your first frame or an average
structure prior to 'atomicfluct'.
-Dan
On Fri, Feb 9, 2018 at 2:12 AM, Mac Kevin Braza <mebraza.up.edu.ph> wrote:
> Hello,
>
> I am calculating atomic fluctuation of a GPCR protein using cpptraj
> atomicfluct bfactor. Specifically, I am calculating the backbone
> fluctuation with .CA,C,N of the specific domain I am looking at. However,
> it seems that the B-factor I calculated exceed from >1000 up to >15,000. Is
> this normal?
>
> I attached here the input file I used.
>
> Thank you very much!
>
> Regards,
> Mac Kevin E. Braza
>
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--
-------------------------
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 Fri Feb 09 2018 - 06:00:06 PST
