[gmx-users] Metal interactions with proteins

Justin Lemkul jalemkul at vt.edu
Wed Nov 15 14:29:08 CET 2017

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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