Re: [AMBER] Problem cpptraj Bridging H-Bond analysis

From: Daniel Roe <>
Date: Mon, 20 Jul 2015 11:32:23 -0600


As stated in the manual (Section 29.9.25, Hbond, pg 575):

  Count is the total number of interactions between solute and solvent
(note this can be greater than the total number of frames since for any
given frame more than one solvent molecule can hydrogen bond to the same
place on solute and vice versa)

So this is expected, and is a consequence of tracking solvent in a
non-specific manner. If you want to track specific water-solute
interactions you will have to explicitly specify water with explicit
donor/acceptor masks. Be warned this will greatly increase the data you
generate. Hope this helps,


On Monday, July 20, 2015, Beuerle, Matthias <>

> Hello everyone,
> I have a problem using the hbond function of cpptraj. I try to analyze
> hydrogen bonds bridged by water molecules of my system. My cpptraj script
> is working and the results look correct in principle, however the lifetime
> of some solute-solvent and solute-solvent-solute interactions in the avgout
> and bridgeout files are bigger than one (in terms of fractions of the whole
> simulation length), which obviously can not be true. Solute-Solute H-Bond
> lifetimes are fine. I read that one of the latest bug fixes aimed at
> problems with lifetime of solute-solvent H-Bond however updating to the
> latest version did not help. My system is a protein DNA complex meaning I
> have 3 separate solute molecules. Anyone has a similar problem and or
> solution? Help would be very much appreciated!
> Best regards,
> Matthias
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> AMBER mailing list
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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 Mon Jul 20 2015 - 11:00:02 PDT
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