[gmx-users] Heavy metals parameterisation

[Justin Lemkul]

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

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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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