Hi,
On Tue, Apr 16, 2013 at 11:46 AM, Binwu Zhao <bzhao.ncsu.edu> wrote:
> calculate HB between solute and solvent? If part of the solute is out of
> the primary box, does it mean we won't get the accurate HB between solute
> and water?
To get accurate solute-solvent hydrogen bond information you should
re-image your solute so that is is at the center of the box prior to
running the hbond command. With cpptraj this can be accomplished with
the 'autoimage' command. With ptraj you need to use a combination of
'center' and 'image' commands.
-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 Tue Apr 16 2013 - 11:00:04 PDT
