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

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Thu Jan 15 13:04:51 CET 2009

If you are interested in develop parameters for Fe2+ suitable to your 
system without huge computational efforts, see this reference:

de Araujo, AS; Sonoda, MT; Piro, OE, et al.  JOURNAL OF PHYSICAL 
CHEMISTRY B   Volume: 111   Issue: 9   Pages: 2219-2224


Zhong Zheng escreveu:
> 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?
>  Thanks a lot.
> Zhong Zheng
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Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *

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