Hi,
On Mon, Nov 19, 2012 at 12:52 AM, rahul sarma <rahulsrm4.gmail.com> wrote:
> The problem is that the structure of the peptide is
> different (showing turn
> in contrast to alpha-helix) after the script is run. Note that, the
> residue numbers
> for the peptide is 1 to 25 and the system contains a Na+ ion (residue
> number 26).
Trajout should not change secondary structure as it does not do any
manipulation of coordinates. What are you using to measure the
difference in structure (DSSP, STRIDE, etc)?
-Dan
--
-------------------------
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 Mon Nov 19 2012 - 09:00:03 PST
