Hi,
On Fri, Mar 6, 2015 at 10:44 AM, George Tzotzos <gtzotzos.me.com> wrote:
> My question is why does the script above (ligand mask included) produce h-bonds with the solvent only but now with Trp114, Phe123 and Trp240?
I think the Amber 14 manual has a decent description of how the atom
masks work in the cpptraj hbond command. In the first case (where the
mask :126,252 is given) you restrict your donor/acceptor search to
those two residues, and consequently obtain only hydrogen bonds
including those two residues. If you don't specify a mask (your second
case), as stated in the manual:
"all solute atoms if no mask speciļ¬ed"
which is why you get more hydrogen bonds.
Hope this helps,
-Dan
>
> Thank you in advance for any comments/suggestions
>
> Regards
>
> George
>
>
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--
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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/
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Received on Sat Mar 07 2015 - 15:00:02 PST
