[gmx-users] How to treat an isolated iron (Fe 2+)

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 15 11:48:59 CET 2009

Zhong Zheng wrote:
> hi all
> I have an isolated iron in the protein. If I don't' put that iron in, 
> everything runs through fine. However, if I put the iron in, the mdrun 
> step (doing energy minimization) will clash. It says segmentation fault 
> and lots of LINCS WARNING. The iron has a +2 charge with four His 
> ligands and one Glu ligand. The total charge for the complex should be 
> +1. Is there a good way to treat this isolated iron?

You may be in for some parameterization, which, for transition metals, can be 
quite complicated:



>  Thanks a lot.
> Zhong Zheng
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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