[gmx-users] Metal interactions with proteins

[Justin Lemkul]

On 11/15/17 6:44 AM, RAHUL SURESH wrote:
> Hello users
>
> I am performing Metal-protein interactions with Charmm36ff using gromacs.
> The metals under study are Cu and Ag in +2 state. Is it sufficient to add
> the topology,i.e the necessary parameters (LJ-potentials) in nonbonded.itp
> and ions.itp alone?

Yes (unless you want pdb2gmx to deal with them, in which case they need 
to be defined in atomtypes.atp, as well). Whether or not those 
parameters are a suitable model of reality is another matter (no 
classical MD force field treats transition metals particularly well).

> In case of nonbonded.itp file, i find charge for most atom types are
> mentioned to be 0.000 and in the line
> *" ; Updated Mg2+ parameters by Allner et al. (DOI: 10.1021/ct3000734)MGA
> 12      24.305000    0.000  A   0.277000    0.01234280 " *the charge for
> this ion is also mentioned to be 0.000 and atom type is refered as MG*A. *What
> does this MGA refers to and why is the charge 0 for this ions.

MGA is the atom type for Mg2+ with the parameters by Allner et al. in 
the linked paper. We have to distinguish between that Mg2+ type and the 
official, "standard" Mg2+ CHARMM36 ion type.

Charges in this file are never used for anything. The column is a relic 
of an ancient idea for building molecules.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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