[gmx-users] metal-surfactant ligand topology

[Justin Lemkul]

On 1/28/16 3:27 PM, Parthiban Marimuthu wrote:
> Hi,
> Can anyone suggest how to prepare topology files for
> metal(Cobalt)-surfactant ligand complex
> I tried the classical tools, prodrg, antechamber and ATB, but cant fix it.

Because no force field supports something weird like cobalt by default.

There are supposedly AMBER parameters for cobalt hexamine 
(http://sites.pharmacy.manchester.ac.uk/bryce/amber) but I have no idea how good 
they are.

In general: http://www.gromacs.org/Documentation/How-tos/Parameterization

Sometimes you have to do the hard work yourself.  I think it unlikely that any 
additive force field will describe cobalt properly.  Even polarizable models may 
be difficult to derive, as is often the case with multiply charged ions.

-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 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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