Thanks for the suggestion, Francesco. I was not aware the RED server could handle difficult cases like this. Will look at it again.
Sergio
-----Original Message-----
From: francesco oteri [mailto:francesco.oteri.gmail.com]
Sent: Wednesday, June 05, 2013 2:18 PM
To: AMBER Mailing List
Subject: Re: [AMBER] iron-sulfur parameterization
Hello,
Sergio, if you need just charges, you can try RED Server.
It works pretty well and permits to manage a huge variety of moleucles.
I used it to get charges for a FeS cluster and the linked Cysteines.
Francesco
2013/6/5 Sergio R Aragon <aragons.sfsu.edu>
> Hello Prof. Case,
>
> I am aware that you are an expert on iron sulfur complexes found in
> proteins and have located one of your classic papers on the issue
> (Noddleman & Case, Adv. Inorg. Chem. 38:423-458 (1992)) but our
> library does not have a copy of this series (hard to believe, I know).
> Do you by any chance have a reprint you could share?
>
> I have been studying Xanthine oxidase (1FIQ), a protein that contains
> an
> Fe2S2 group, one of the smaller of such clusters. I am quite well
> aware of the need to revise the parameters for the CYS residues that
> connect this cluster to the protein, but it is not clear to me how to
> do this. If I carry out an Oniom calculation in g09, I can include
> these CYS residues and eventually perhaps get ESP charges for the
> whole set of atoms that include the cluster and the CYS residues.
> However such a procedure does not guarantee that the partial charges
> are consistent with those assigned to the rest of the protein. I am
> hoping that by reading your paper I can have a handle on the charge
> state to assign to this smaller iron-sulfur cluster, as that is not
> clear to me either. I have no experience in the full development of
> force field parameters yet - it seems that this problem requires me to learn about that.
>
> If you have any material that is relevant to this iron-sulfur complex
> that you could share, or specific suggestions, I would be much appreciative.
>
> Thanks,
>
> Sergio Aragon
> Professor of Chemistry
> San Francisco State University
>
>
> -----Original Message-----
> From: case [mailto:case.biomaps.rutgers.edu]
> Sent: Wednesday, June 05, 2013 12:41 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] iron-sulfur parameterization
>
> On Thu, Jun 06, 2013, venkatesh s wrote:
> >
> > i am struggling with iron-sulfur cluster
> parametrization
> > Unknown residue: SF4 number: 0 type: Terminal/last
>
> This is a difficult problem: iron sulfur cubane clusters come in three
> oxidation states, and reliable vibrational spectra have only recently
> become available. One not only needs parameters for FS4, but also
> revised parameters for the four CYS residues that are connects to the
> iron-sulfur cubane.
>
> We are working to prepare a set of files that will allow such active
> sites to be modeled, but this is still a work in progress, and more
> testing is needed.
>
> Some CHARMM force field parameters for the 2- state are discussed by
> Mitra et al. Biochemistry 50:5220, 2011. These may help, but you will
> need to know a lot about force fields and how they are represented in
> Amber parameter files. It's not just a matter of loading a PDB file.
>
> ...regards...dac
>
>
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--
Cordiali saluti, Dr.Oteri Francesco
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Received on Wed Jun 05 2013 - 15:30:02 PDT
