Hi,
If you use the cpptraj 'hbond' command with the 'nointramol' keyword
it should do a reasonable job determining hydrogen bond donors and
acceptors.
-Dan
On Sun, Dec 14, 2014 at 8:40 PM, maryam azimzadehirani
<maryamai1988.gmail.com> wrote:
> Dear Amber users,
> Does anyone know how we specify the H-bonds donors and acceptors in ptraj,
> while calculating the H-bonds between glycans(sugar residues) and Protein?
> Regards,
> Maryam
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Sun Dec 14 2014 - 20:30:03 PST
