Hi,
The 'secstruct' command in cpptraj/ptraj will calculate secondary
structure according to the DSSP algorithm of Kabsch and Sander. You
can get both secondary structure vs time and overall average secondary
structure. See the AmberTools 13 manual for more details.
-Dan
On Wed, Aug 7, 2013 at 10:56 AM, Chinthaka Ratnaweera <cnr88.msstate.edu> wrote:
> Hi
> Can anyone let me know that the best way to analyze the changes in
> secondary structures of a protein during a MD run.
> Thank You
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Aug 07 2013 - 10:30:04 PDT
