[gmx-users] Force field for Cobalt topology??
jalemkul at vt.edu
Mon Feb 6 15:58:20 CET 2017
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
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
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