Thank you very much for your reply. Actually, I am observing the peptide in
VMD where
I see this discrepancy.
Rahul
On Mon, Nov 19, 2012 at 8:33 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 20:30:02 PST
