[gmx-users] Protein simulation including ligand with Fe(III)

Justin Lemkul jalemkul at vt.edu
Wed Aug 6 16:38:12 CEST 2014

On 8/6/14, 8:19 AM, Nikolaos Michelarakis wrote:
> Hello again,
> Since I could not find any reliable parameters for the Fe-O for the GROMOS
> 96 forcefield I decided to modify it to use the parameters for its Fe-N in
> its HEME group. While reading through the gromos54a7 files i saw that it
> has parameters for the Fe-O bond so I thought that it might be able to deal
> with my molecule. I run pdb2gmx on my molecule, which included the protein
> and the iron, and a topology was produced, giving no errors. However, when
> I opened the topology, there is no Fe present in it. Sorry if that's a
> silly question but shouldn't it be in there? I can include the files if
> required.

Indeed, that makes no sense at all.  Please post the topology and input 
coordinate files for download on a file-sharing service.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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