[gmx-users] Help with respect to processing protein with FE2+

Justin Lemkul jalemkul at vt.edu
Mon Dec 24 19:43:55 CET 2018

On 12/24/18 10:11 AM, Prasanth G, Research Scholar wrote:
> Dear all,
> One of the proteins of my interest, has a FE2+ in the center and as it
> plays a main role in the activity of the protein, it cannot be removed.
> Can you please suggest a solution. I have tried with CHARMM and GROMOS,
> with no success.
> After reading a bit, I understood that, the charges on the ions cannot be
> represented effectively as we generalized the residues as spheres and ions
> cannot be represented with such a generalization. But, i have not found any
> solution as to how to edit the protein.pdb file, so that the program
> accepts it.

The CHARMM and GROMOS force fields support Fe2+ in the context of a heme 
residue. Anything else would not yet be parametrized. You are right that 
a divalent transition metal will inherently alter the properties of 
species around it (ligating residues, etc) but the only real solution 
for that is QM/MM if those behaviors are relevant to what you're 
interested in.

If the Fe ion/atom is part of some larger cofactor, you'll either have 
to parametrize it (potentially arduous, given the limitations of 
additive force fields) or treat it quantum mechanically.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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


More information about the gromacs.org_gmx-users mailing list