[gmx-users] Force field for Cobalt topology??

[Justin Lemkul]

On 2/6/17 9:08 AM, Amir Zeb wrote:
> Hello gmx users,
>
> I'm wondering which would be the best force field to create topology for
> cobalt. I tried different ff but none of them get the task. I searched the
> mailing archive too but I couldn't get the way to solve the issue.
> Dr. Justin has just mentioned (https://www.mail-archive.com/gmx
> users at gromacs.org/msg46374.html) that there is no such suitable force field
> yet to deal with transition metals correctly due to their lack of fixed
> charge. But this was commented so back.
> Let me know if the recent advances had solved such issue.
>

The link doesn't point to a valid page, so I don't know the context or content 
of that post, but I can probably guess :)  I may be repeating myself, but here goes:

Transition metals are challenging for additive MD force fields.  There are 
issues of polarization, charge transfer, and coordination (which can be flexible 
and ligand-dependent).  Additive MD force fields are quite crude in this regard 
and often can't capture such effects (heck, even "common" ions like Ca2+ and 
Mg2+ are often represented very poorly, let alone harder things like transition 
elements).  QM/MM may be a solution, in which you treat the cobalt and ligating 
residues as a QM region and the rest of the system as MM, but it depends on what 
you're doing as to whether or not you want to invest a lot of time in such an 
effort.

-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

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