Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug

From: Daniel Roe <>
Date: Mon, 22 Sep 2014 08:24:06 -0600


On Mon, Sep 22, 2014 at 12:37 AM, <> wrote:
> I was comparing my Hbond outputs using the Hbond command from both
> ambertools12, and ambertools14.
> There was discrepency for hydrogen bonding for some types of hydrogen
> bonding between them.
> 1. H of water and O of protein was found to be the same
> 2. H of bound to O/N of protein and O of water was found to have very high
> fractions up to 2.5 compared to an expected maximum of ~1.

The AmberTools 12 version of cpptraj didn't have the 'solventdonor'
and 'solventacceptor' keywords implemented, so I'm not sure how you
are even comparing them. Without knowing what input you gave to the
AT12 version of cpptraj I can't really answer this.

> Attached is the relevant files.
> A view of the trajectory in VMD shows hydrogen bonding to only 1 water O by
> the H most of the time, not 2.5 .

The 'solventacceptor' and 'solventdonor' keywords track *any*
solvent-solute hydrogen bond, which is why the fraction can be greater
than 1. You don't say what criteria you're using in VMD, but note that
the default values in VMD are more strict than the criteria you gave
cpptraj, which may be why you see more hydrogen bonding in the latter.
In VMD the defaults are distance 3.0 Ang., angle 20 (in VMD the angle
is the deviation from 180). However, in your cpptraj run you specified
distance 3.5, angle 120 (which is equivalent to angle 60 in VMD
terms). What happens if you give distance 3.0, angle 160 to cpptraj?


> Lee Xiong An
> _______________________________________________
> AMBER mailing list

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 Sep 22 2014 - 07:30:05 PDT
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