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

[Justin A. Lemkul]

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:

http://wiki.gromacs.org/index.php/Parameterization
http://wiki.gromacs.org/index.php/Exotic_Species

-Justin

>  Thanks a lot.
> 
> 
> Zhong Zheng
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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