Re: [AMBER] hbond analysis - bridgeout

From: Daniel Roe <>
Date: Thu, 11 Jul 2013 17:18:01 -0600


On Thu, Jul 11, 2013 at 5:09 PM, Fabrício Bracht <> wrote:
> between residues. Does hbond identify if two residues are bridged by more
> than one water molecule, i.e., an interaction of the type "RES1 - WAT - WAT
> - RES2" ?

No, currently the code looks for single bridging water molecules only.
As you can imagine the book-keeping becomes much more complicated when
you consider 2+ bridging molecules (since now you have to look at all
solvent-solvent hbonds as well). I wouldn't rule putting this
functionality in at some point, but it's complicated enough that it
likely won't be available in the immediate future.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
AMBER mailing list
Received on Thu Jul 11 2013 - 16:30:03 PDT
Custom Search