Hi,
You can use the 'secstruct' command in cpptraj to calculate secondary
structure (it uses the DSSP algorithm). See the manual for complete details.
-Dan
On Tue, Mar 18, 2014 at 5:23 AM, Tanmoy Paul <tanmoy635.gmail.com> wrote:
> Dear amber users ,
> I am trying to calculate the percentage of
> secondary structure of any protein ( not per residue ) from .mdcrd file.
> Now most of the online servers like DSSP, Stride takes pbd file as input.
> But I have 10000 frames in the mdcrd file . So it is very difficult to
> covert all those frames into pdb and than do the analysis . Can anybody
> suggest me anything that can help ?
>
>
> Regards
>
> Tanmoy
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--
-------------------------
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) 585-6208 (Fax)
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Received on Tue Mar 18 2014 - 07:30:04 PDT
