[gmx-users] hbond hydroxyl oxygen, both acceptor and donor?

[Justin Lemkul]

On 7/18/16 4:27 PM, Jeremy T First wrote:
> Hello,
>
> I am attempting to quantify the amount of hydrogen bonding environment a
> certain residue experiences during the course of a simulation. To do this,
> I am using gmx hbond to plot the number of hydrogen bonds between the
> solvent (water) and the hydroxyl oxygen of the residue as a function of
> simulation time.
>
> According to the help information for gmx hbond, hydroxyl oxygens are
> classified as hydrogen bond donors. When I select this oxygen and the Water
> group in gmx hbond, gromacs finds one less donor than acceptor, leading me
> to believe that the hydroxyl oxygen is classified only as a donor, and not
> also as an acceptor.
>
> Many frames of my simulation show the hydroxyl oxygen (as calculated by
> VMD) donating and accepting a hydrogen bond, but gmx hbond only reports 1
> hydrogen bond for the frame.
>
> Is there any reason that a hydroxyl oxygen can not simultaneously donate
> and accept a hydrogen bond? If not, is there a way to let gromacs allow the
> hydroxyl oxygen to be an acceptor as well?
>
> Any help would be greatly appreciated!
>

You can't use just the oxygen atom; the analysis group must contain both O and H 
to be considered a donor.  If you're just selecting an O and the entire water 
group, the O in the hydroxyl can only be considered an acceptor.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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