AMBER Archive (2009)

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

From: FyD (
Date: Sat May 02 2009 - 11:02:48 CDT

Dear Hao,

> In the parameter file, frcmod.hemall (/dat/contrib/heme), I find that the
> total charge of the Fe-heme is -2.

You can see that iron presents only 4 ligands, here.

> 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?

-1 x 2 (2 nitrogens) - 1 x 2 (2 propionates) = -4
-4 + Fe-II_? = -2

> Besides, I try to use antechamber to generate the partial charge for
> Fe-heme. Firstly, a gaussian calculation is performed to generate the
> electrostatic potential. After that, when I use the command: "antechamber -i
> hem.log -fi gout -o hem.prepin -fo prepi -c resp", the following message can
> be found, and the .prepin file can not be generated:
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly
> increase the computer time

Antechamber does not deal with metals.

> Can anyone give some help?

You can use R.E.D.
See R.E.D., R.E.D. Server, R.E.DD.B. & tutorials

regards, Francois

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