Re: [AMBER] cpptraj H-bond: clarification sought

From: Daniel Roe <>
Date: Sat, 7 Mar 2015 15:38:03 -0700


On Fri, Mar 6, 2015 at 10:44 AM, George Tzotzos <> 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,


> Thank you in advance for any comments/suggestions
> Regards
> George
> _______________________________________________
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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
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Mar 07 2015 - 15:00:02 PST
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