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

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Wed Jan 23 11:08:23 CET 2019


Dear Justin,

I had installed ambertools and followed the tutorial -
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm
Currently, I am using gaussian to run the optimization part for obtaining
parameters. During the process, I realized that the ligand is not picked up
as a residue interacting with the metal ion (during the preparation of
input files for gaussian).

My question is, is it advisable to convert the resultant files obtained
from amber and convert it into cgenff compatible files using tools already
available?
Can I then switch over to GROMACS and use cgenff forcefield for running the
simulation?


Quoting your previous response -
---------------------------------------------------------------------------

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

On Mon, Dec 24, 2018 at 8:41 PM Prasanth G, Research Scholar <
prasanthghanta at sssihl.edu.in> 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.
>
>
>
-- 
Regards,
Prasanth.


More information about the gromacs.org_gmx-users mailing list