[gmx-users] hbond between backbone atoms

[Justin Lemkul]

On 6/28/16 6:41 AM, Ming Tang wrote:
> Dear list,
>
> I want to calculate hbond between backbone atoms on different chains of my protein only. but when it give me this error "nothing to be none".
> I used this command: gxm hbond -f traj.trr  -s topol.tpr -num hbnum.xvg -a 30  -r 0.5
> I can use this command to get hbond between protein and protein.
> Can anybody give me some suggestions?
>

Use Mainchain+H.  Backbone considers only C+CA+N, so there can be no H-bonds in 
those atoms.  MainChain+H is C+CA+N+H+O, which includes what you actually want.

-Justin

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

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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