Re: [AMBER] hbond analysis - bridgeout

From: Daniel Roe <>
Date: Thu, 11 Jul 2013 13:00:05 -0600

On Thu, Jul 11, 2013 at 12:04 PM, Fabrício Bracht <> wrote:
> that are bridged. For the number of water molecules involved in this link
> and the identity of them, I have to look at the raw "out" file. Isn't there
> a way to obtain such info in a more organized fashion?

#Frame hb[UU] hb[UV] hb[Bridge]
       1 5 27 3

I feel like this format is pretty organized, considering that every
frame you can have a different number of solvent molecules bridging 2
or more solute residues. This line tells me I have 3 bridging solvent
molecules: solvent residue 208 bridging solute residues 10 and 11,
solvent residue 494 bridging residues 2 and 3, etc. The information is
contained in a single string that is readily parsable by your favorite
text manipulation language so you can organize it into any format you
prefer (I would probably just use awk).


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)
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Received on Thu Jul 11 2013 - 12:30:03 PDT
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