[gmx-users] Protein simulation including ligand with Fe(III)

[Justin Lemkul]

On 8/5/14, 6:43 AM, Nikolaos Michelarakis wrote:
> Hi Justin,
>
> Thank you for your answer. I was going to use the parameters from an MM
> paper but since you mentioned that, any idea where I can find some better
> parameters? I don't want them to be perfect and I don't have time for QM,
> just something so the protein won't blow up up.
>

If you've got something that's published and seems to be reliable, that's 
probably the best you can do, but MM misses many important effects and the fixed 
charge of +3 on a coordinated Fe ion is a bad approximation, in general.  That's 
nothing you can hope to fix with additive MD, but just be aware of the possible 
shortcomings of the model.

-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 601
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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