AMBER Archive (2006)

Subject: Re: AMBER: RESP charges of iron-porphyrin system

From: Shin Tokumoto (stokumoto_at_tara.tsukuba.ac.jp)
Date: Thu Dec 14 2006 - 03:31:13 CST

Dear AMBER users,

Two month ago, I submitted a question concerning the RESP
calculation; when an Fe ion is included in the system (such as a
heme), the partial charge for the Fe ion is not calculated by the
Antechamber system.

I saw the source code of the RESP program, and knew that the
bond is recognized via the atomic distance; since in my case, the
bond length of the Fe-N bond is too long than the critical distance,
it was not set as a covalent bond in the program.

So, for the Fe-N bond, I specifically gave the bond information in
the program, independently on the above scheme for the bond
recognition. Thus, I obtained the approapriate value for the partial
charge of the Fe ion.

Shin Tokumoto
University of Tsukuba

Shin Tokumoto wrote:
> Dear Amber users,
>
> Regarding RESP charge of Fe, I have a question.
>
> I would like to calculate RESP charges of iron-porphyrin system.
> First I performed Gaussian03 on this iron-porphyrin system, adding to
> the input
> file both a keyword, "pop=readradii", and the value of Fe V.D.W radius
> to get the
> electrostatic potential. By using the output file, I then performed
> antechamber and
> could get a prep file. But there was no information about the Fe RESP
> charge in this file,
> that is to say, the corresponding place is empty.
>
> Would you tell me how to get the correct RESP charge of Fe?
>
> Thanks for any help.
>
> Shin tokumoto.
>
>
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