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

[Justin Lemkul]

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

-- 
==================================================

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
http://www.thelemkullab.com

==================================================