[gmx-users] Modifying the force field to recognize iron with ligand atoms?

Justin Lemkul jalemkul at vt.edu
Tue Nov 13 14:32:09 CET 2012

On 11/12/12 9:17 PM, Rajiv Gandhi wrote:
> Could someone tell how can i modify the specific force field, for example
> gromacs43a1, to build topology file for protein has iron that interact with
> some ligands (cytochrome, hemoglobin...etc)? which file i should modify?

Heme parameters already exist in the Gromos force fields.  There are some 
missing bonded parameters, as I recall, but people have used them for 
simulations, so I suspect the necessary information is somewhere in the 
literature.  For searching purposes, it's best to use the correct terminology - 
there's no such thing as a "Gromacs force field."  The one you reference is 
Gromos96 43A1, which is a specific parameter set within the Gromos96 family of 
force fields.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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