[gmx-users] Why h_bond can not form

Justin Lemkul jalemkul at vt.edu
Mon May 11 13:46:38 CEST 2015

On 5/10/15 8:48 PM, 范聪 wrote:
> Hello everyone!
> I offered a picture called "ask.png" to illistrate my question.
>   According to the referense papers, the H atom of the -OH group of TYR306 should form H_bond with the carbonyl O atom of the ligand.

Depending on the methods used in those papers, maybe that hypothesis isn't right :)

>   But in my simulations, the H atom turned after a very short time, towards the side chain of PHE152.
> I guess the reason is that, first, the positive Zn ion near the ligand's carbonyl O atom made a repulsive effect against the H atom in -OH group; second, the π-electron cloud of the side chain of PHE attracted the H atom in the -OH group of TYR306.

I wouldn't put any stock in any arguments about pi electron clouds in MD 
simulations.  QM/MM shows clearly that the assignment of +2 charge to bound 
metals is very crude and often a poor model of reality.

>   As a whole, I failed to make out a real-enough simulation because the h_bond between the ligand and TYR306 did not form.

This could also be a force field issue, in general.

>   Also I have one more question: Is there any tools or solutions to calculate the hydrophobic or π-π interactions between the ligand and seleted residues of the protein, so I could make a graph of the interactions against time?

You can map contacts, angles between the rings, etc.  See the manual for 
available tools and discussions in the archive on these exact topics.



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


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