Re: [AMBER] trajout command in ptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 19 Nov 2012 09:33:50 -0700

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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 19 2012 - 09:00:03 PST
Custom Search