[gmx-users] g_hbond

[Justin Lemkul]

On 6/20/14, 6:23 AM, Nidhi Katyal wrote:
> Hi all,
>
> I have created hydrogen bond existence map. In the index file generated
> using hbn option I can see following lines at the end:
>     1      2   1598
>        1      2   1851
>        1      2   1852
>        1      2   1862
>       10     11   1643
>       10     11   1651
>       10     11   1658
>       10     11   1664
>       10     11   1682
>       10     11   1748
>       10     11   1754
>       10     11   1761
>       10     11   1762
>       10     11   1772
>       10     11   1830
>       10     11   1831
>       10     11   1838
>       10     11   1851
>       10     11   1862
>
> There are 19 lines in total and also in the existence map created using hbm
> option, I could see 19 lines. But when I generate index file with a2 and
> calculate hydrogen bond with my ligand moleules, I can see zero bonds. Am I
> doing something wrong?
>

You can't calculate hydrogen bonds with a single atom.  The donor-acceptor 
distance is used as part of the criteria.  The output indicates that atoms 1 and 
2 serve as the donor, and 1598 etc. are the acceptors.  To analyze hydrogen 
bonds of a specific group, you need the donor and associated H in a single group.

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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