Hi,
On Sat, Sep 7, 2013 at 1:19 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
> sir,
> On doing hbond analysis (including solvent effect), should i image center
> familiar solvent residues also? (simulation is done with iwrap=1). would it
> affect my analysis.
If you are looking for solvent-solute hydrogen bonds you should
definitely reimage prior to 'hbond' since neither ptraj nor cpptraj
use imaged distances in the 'hbond' command; in cpptraj I recommend
using 'autoimage' for this purpose.
-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 Sat Sep 07 2013 - 09:30:03 PDT
