[gmx-users] Iron containing structure simulation crash

Justin Lemkul jalemkul at vt.edu
Tue Aug 12 23:23:15 CEST 2014

On 8/12/14, 1:57 PM, Nikolaos Michelarakis wrote:
> Thank you very much for your answer!
> this is the link to the whole forcefield directory:
> https://drive.google.com/folderview?id=0Bxa-J2wEpEeqbnZDVmpmQ0JGcUE&usp=sharing
> Since it's my first time doing something like that, i might have done
> something wrong in adding the iron in the forcefield. Since iron was
> already present in the heme group of the forcefield i used FE3+ as a name.
> please let me know if I have done something wrong.
> I tried playing around with the charge of the iron, changed it to 0.4, and
> these are the new files i got for every step, along with the topology. This
> time the force on the whole structure was larger and a lot smaller on the
> oxygen bound on the iron:
> https://drive.google.com/folderview?id=0Bxa-J2wEpEeqME82TjhJUnQ0TzQ&usp=sharing
> I would appreciate it If you could take a look at the forcefield and let me
> know if everything is correct in there and I will try finding the correct
> parameters.

Without looking at the parameters at all, there are a couple things to note:

1. The protonation of His227 is wrong.  The epsilon N atom is what coordinates 
the Fe ion.  It certainly shouldn't be protonated; set it to delta protonation 
with pdb2gmx.  You're getting repulsion between the positively charged H and the 
Fe ion.

2. The Fe site is a bit strange in that it has 3 Arg nearby, which will 
certainly contribute to repulsion.

3. The pKa of Tyr will probably be affected by the Fe ion.  It may even be 
deprotonated under such conditions.

The net effect is you need to be doing some detailed QM calculations and 
significant force field parametrization here.  Whatever you found in the force 
field is going to be inadequate.  If the Fe parameters were developed for heme, 
they are certainly not applicable here with such a different chemical environment.



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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