[gmx-users] Metalloenzyme MD

[Reza Esmaeili]

Thanks a lot Justin for being helpful here too.
 🙏🙏
> On Jan 31, 2017, at 21:35, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 1/31/17 1:54 AM, Reza Esmaeili wrote:
>> I’m trying to simulate a metalloenzyme containing an Fe2+.
>> What is the best way to make the Fe2+ stay in its place and not scape the position?
> 
> You will need to carefully parametrize bonded interactions between ligating atoms and the ion, or at minimum set up a system of distance restraints.  Or there's always QM/MM, but that's a considerable time investment in just doing those runs, so it depends on what the purpose of your simulation is.
> 
> -Justin
> 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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