[gmx-users] How to interpret gmx H_bond analysis?

[Justin Lemkul]

On 6/13/17 11:25 AM, Adarsh V. K. wrote:
> Dear gmx users,
> 
> How to interpret gmx H_bond analysis?
> 
> I have done 20 ns simulation of a protein-ligand complex
> (Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in
> several frames during the first 2ns of simulation. But from 2 ns onwards
> consistent (at least one) H bonds are seen till the end of simulation (Is
> this due to restraining of ligand?)
> 
> How can we interpret this protein-ligand simulation.
> 
> Whether the ligand will 'fall off' from the protein during the first 2 ns
> of simulation since there are many zero H bonds till reaching 2 ns?
> Why consistent H bonds after 2ns seen ?
> 

I answered this a couple of days ago:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-June/113678.html

-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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