Hi,
You can use cpptraj to perform analysis of your trajectories. RMSF can
be calculated with the 'atomicfluct' command, and secondary structure
can be calculated with the 'secstruct' command (employs DSSP
algorithm). See the manual for command details.
Also, you may want to try the beginner analysis tutorials:
http://ambermd.org/tutorials/analysis/
-Dan
On Mon, Mar 23, 2015 at 12:45 PM, shahab shariati
<shahab.shariati.gmail.com> wrote:
> Dear amber users
>
> I am beginner in amber.
>
> I have experience with gromacs.
>
> I did md simulation of my system (protein).
>
> I want to do following analysis:
>
> RMSF
> changes of the secondary structure of protein
>
> Can I use amber for these analysis?
>
> Any help will highly appreciated.
>
> Best wishes,
> Shahab
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Mar 23 2015 - 12:00:03 PDT
