[gmx-users] Fwd: Topology error

Justin Lemkul jalemkul at vt.edu
Mon May 22 13:16:19 CEST 2017

On 5/22/17 6:55 AM, Jai Krishna wrote:
> Dear Sir/Ma'am,
> I am trying to generate topology file for my metalloprotein that has FeS
> cluster and Fe2+ atoms in it. When I run the pdb2gmx command, it fails to
> generate the topology file. The error says -   Residue 'FE2' not found in
> residue topology database.
> Could you please help me with this query? What steps should I take to
> proceed forward with it. I also like to tell you that I need these atoms in
> my protein for ligand to bind and for simulation also.

This is a very difficult issue.  Additive force fields do not treat multivalent 
ions well, and transition elements are extremely challenging due to their 
complex real world behavior.  Hence any parameters that a given force field 
might have for something like Fe2+ are probably only going to be in the context 
of heme, which also likely has covalent bonds between Fe2+ and ligating atoms 
because the nonbonded treatment is badly inadequate.

The FeS cluster is even worse.  You'd have to parametrize that, along with the 
ligating residues, due to the considerable effects of polarization and charge 
transfer.  Some efforts may be made in parts of the literature, so do some 
homework first, but often these kinds of cases are treated with QM/MM to 
side-step the force field issue.  Whereas parametrizing new species (ligands, 
modified residues) is considered an expert topic, anything to do with transition 
elements and cofactors like these would be an expert expert topic.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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