[gmx-users] Donor acceptor detection

[Justin Lemkul]

On 6/10/15 12:38 AM, Parvez Mh wrote:
> Dear users and admin,
>
>             My system consists of -NH and -OH functional group. Atom names
> are N23, H24(attach to nitrogen) and O25 and H26(attach to O). I want to do
> hydrogen bond analysis. I created two index group using make_ndx in
> following way
> a N23 | a H24
> and
> a O25 |  H26
>
> I choose N23_H24 as first selection and O25_H26 as second selection. I am
> curious if i am correct analyzing hydrogen bond between two group. I am

Seems fine.

> also curious how do gromacs detect donor and acceptor or Hydrogen attach to
> donor(that is important for angle measurement). Does gromacs detect first
> letter in atom name like N in N23 to detect ?

Yes.

-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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