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