[gmx-users] Metal interactions with proteins
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.
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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