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

[Justin Lemkul]

On 6/10/17 12:37 AM, Adarsh V. K. wrote:
> Dear gmx users,
> 
> How to interpret gmx H_bond analysis?
> 
> I have done 20 ns position restrained 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? The consistent H bonds after 2ns seen due to restraining of
> ligand while performing simulation?
> 

Watch the trajectory and see what happens.  Try to be more selective in 
analyzing different groups of the ligand if you're only analyzing the ligand as 
a whole to get more insight into what's going on.

-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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