[gmx-users] Simulation with ligand on protein surface

Justin Lemkul jalemkul at vt.edu
Fri Jul 10 23:09:35 CEST 2015

On 7/10/15 5:02 AM, az wrote:
> Hi all
> I was wondering if anyone had experience/pointers regarding simulating
> protein-ligand systems where the interface was heavily surface-exposed ?
> I've been running quite a few of those these days with Amber99SB--ildn, TIP3P,
> and acpype (i.e. Ambertools) for ligand parametrization, mainly for the purpose
> of probing stability of peptidomimetic docking poses (10-50ns; aside from the
> force-field I follow Justin Lemkul's tutorial quite closely). Having however
> noticed that some of my reference ligands (i.e. ones with crystallographic/NMR
> data) wander away from where they should remain, I started wondering whether
> there could be something wrong with my setup. I obviously understand there's a
> zillion possibilities here, but I was still wondering whether there exists some
> sort of 'good-practice' for such cases (e.g. choice of force-fields,
> equilibration protocols ... anything really). I cannot be the only one doing
> this and if anyone has a protocol that served them well in the past, I'd love to
> learn about it.

In general, if an interaction is not preserved, that suggests a poor 
parametrization of that ligand.  But "wander away" is a bit vague; if it's just 
a small reorientation or something, it may not actually be "wrong" at all. 
Depends on the quality of the experimental data and the agreement with 
experimental conditions, as well.



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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