[gmx-users] Heavy metals parameterisation
jalemkul at vt.edu
Tue Apr 11 14:52:53 CEST 2017
On 4/11/17 8:44 AM, Alex Mathew wrote:
> Dear Justin,
> More specifically, I'm looking for the transport properties of proteins in
> presence and absence of heavy metals- how heavy metals affecting the
> transportation of molecules across the channels.
Are the transition metals bound to any specific protein moieties? Free to float
around in the solvent and you hope to see some inhibitory effect? If the former,
that's a reasonable application for QM/MM, albeit still expensive so it may not
be practical to try to run. If the latter, it's really not feasible; you'd have
to actually do all the force field parametrization work to balance interactions
with protein moieties to ensure that the physics is modeled reasonably. Of
course, the additive representation is still very crude for multivalent ions so
this could be a very difficult endeavor.
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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