Hi,
Check out the 'contacts' command in CPPTRAJ/PTRAJ. This will determine
contacts as distances between atom pairs using a mask and a distance
cutoff based on either a reference frame or the first frame of your
trajectory. See the AmberTools 13 manual for more details.
-Dan
On Fri, Aug 23, 2013 at 6:44 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am working with protein-ligand interaction. I would like to calculate the
> number of contacts ligand make with the protein within a specific cut off (
> say within 3.5 to 4.5 angstroms), along the simulation trajectories. How
> can I get help from PTRAJ/CPPTRAJ for doing this calculation?.
>
> Thanks in advance
>
> Regards
> Anu
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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) 585-9119 (Fax)
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Received on Fri Aug 23 2013 - 09:00:03 PDT
