AMBER Archive (2009)

Subject: Re: [AMBER] charge of Fe-heme

From: David A. Case (
Date: Fri May 01 2009 - 17:52:45 CDT

On Fri, May 01, 2009, 董昊 wrote:
> In the parameter file, frcmod.hemall (/dat/contrib/heme), I find that the
> total charge of the Fe-heme is -2.
> When binded to Fe, the porphine are deprotonated, so the charge on porphine
> should be -2. For the central Fe, both Fe(II) and Fe(III) are possible. But
> only Fe(II) can bind to O2. Anyway, the total charge of Fe-heme should be 0
> (Fe(II)) or +1 (Fe(III)), depending on the formal oxdation number of the
> central. However, why the total charge of Fe-heme in amber force field is
> -2?

There are two propionic acid groups on the porphyrin (this is *not* porphine).

> Besides, I try to use antechamber to generate the partial charge for
> Fe-heme.

Antechamber will not work with metal atoms. I agree that error messages
could/should be clearer here.


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