[gmx-users] Heavy metals parameterisation

[Justin Lemkul]

On 4/11/17 8:59 AM, Alex Mathew wrote:
> I'm looking something like this
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856166/
>
> Here the mercury bind to Cys residue and inhibiting the channel.
>

I suggest following a similar method to develop force field parameters, but 
consistent with CHARMM, not AMBER (they use different QM approaches).  But note 
that transition metals cause lots of problems in QM; some DFT methods work 
better than MP2.  I'm working on some of this for our polarizable force field 
and it is a major pain to find a consistent model chemistry that's both 
sufficiently accurate and applicable to multiple ions.

-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

==================================================