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

Justin Lemkul jalemkul at vt.edu
Tue Aug 5 03:32:26 CEST 2014

On 8/4/14, 5:10 PM, Nikolaos Michelarakis wrote:
> Hello,
> I want to run a protein simulation where I will include a ligand which has
> an Fe(III) bound on it. So far I have found how to deal with the ligand,
> creating its topology seperately and then adding it. Since I am quite new
> to MD I have some questions on  how to include the Fe(III) and where.
> I have some parameters for the Fe(III) ion. From reading the manual I
> understand that I have to go to the forcefield .atp and other files and add
> the metal parameters there? Is that correct?

Assuming by "other files," you mean ffnonbonded.itp and ffbonded.itp, yes.

> My second question, assuming I have added the parameters successfully, if I
> include the ion, which is bound to the ligand, with my protein, run pdb2gmx
> and then add the ligand topology separately, will the ion be in the correct
> place? It might be a stupid question but I want to make sure. xD

The easiest way to know is to try it.  If all you do is strip the ligand 
coordinates and process the protein with pdb2gmx, then yes, everything will be 
in the right place.  The bigger concern is what parameters you use for Fe(III). 
  Additive MM force fields are pretty bad for such species...



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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