[gmx-users] Advice needed

[Justin Lemkul]

On 3/31/15 5:25 AM, Priya Das wrote:
> Dear all,
>
> I am working with a transmembrane ion channel and have docked a ligand
> which binds to its pore.
> The ligand forms only one hydrogen bond with the ion channel.
> I want to prove the stability of the binding of this ligand using
> protein-ligand dynamics.
>
> 1) Do i need to convey to the system about the hydrogen bonds , i.e.,
> between which atoms are the hydrogen bonds formed ?
>

Hydrogen bonds arise principally due to electrostatic interactions.  You don't 
provide any sort of information about "this is a hydrogen bond" as part of any 
input.

> 2) Is gmx hbonds the command for it?
>

As the name implies, yes.

> 3) In the tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html)
> , there is no mention about forming any hydrogen bonds between ligand and
> protein , then how do we judge that the protein- ligand affinity is stable
> in that site or in that conformation?
>

Hydrogen bonding is one of many possible stabilizing interactions.  There is a 
whole lot more to the story of protein-ligand binding than just hydrogen bonds.

-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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