Re: [AMBER] Hbond analysis

From: Daniel Roe <>
Date: Wed, 30 Oct 2013 13:01:25 -0600


On Wed, Oct 30, 2013 at 12:34 PM, Fabrício Bracht <> wrote:
> with cpptraj. I have specified the analysis along with the options for
> solvent hbond analysis and bridge. Within the hbond between residues, the
> interaction between a carboxylate from an asp residue and the hydrogens
> from the guanidinium group show up like this:
> ASP_204.OD2 ARG_206.HE ARG_206.NE 4228 0.8456 3.0151 145.4176
> ASP_204.OD1 ARG_206.HE ARG_206.NE 4072 0.8144 3.2199 154.9778
> So, the fraction of frames in which OD2 and OD1 stay bonded to the same
> hydrogen atom on arginine is 0.8456 and 0.8144 respectively. How can this
> be so? Shouldn’t the fractions add up to 1?

Remember that hbond is essentially an enhanced version of the
'distance' command, subject to distance and angle cutoffs. Any time
those distance and angle criteria are satisfied, a hydrogen bond is
considered "formed". It's entirely possible that for certain frames,
OD1 and OD2 are close enough to HE satisfy your distance and angle
cutoffs at the same time (you don't specify what your cutoffs were but
I'm assuming at least 3.3 for distance?). Because of this they don't
necessarily have to add up to 1.0.

> I get even more confused when I take into account the other interactions
> that this asp residue does.
> ASP_204.OD2 OH1_342.H1 OH1_342.O 4612 0.9224 2.9481 158.4453
> This is OD2 bonded to a water molecule bound to a zinc complex.
> In the solvent analysis output.
> OH1_342.O SolventH SolventDnr 10182 2.0364
> 2.7305 162.2674
> How can the Hbond appear in 10182 frames if I only analysed 5000?

The hbond section (8.10.18) of the AT13 manual explains this:

"If solvout is specified the average of each solute-solvent hydrogen
bond formed over the course
of the trajectory will be written to <sfilename> in a manner analogous
to avgout. Note that for
solute-solvent hydrogen bonds the ’Frames’ column becomes ’Count’
since for any given
frame more than 1 solvent molecule can bind to the same place on
solvent and vice versa."

So it's likely that there were ~2 solvent molecules in the vicinity of
that OH1_342.O atom.

Hope this helps,


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) 585-6208 (Fax)
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Received on Wed Oct 30 2013 - 12:30:02 PDT
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