Actually, the standard version doesn't. But there is a development version
that handles more complicated situations.
Try to write to the RED mailing list.
They are very nice ;) They helped me a lot!
Francesco
2013/6/6 Sergio R Aragon <aragons.sfsu.edu>
> 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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> >
> >
> >
> > _______________________________________________
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> >
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
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Cordiali saluti, Dr.Oteri Francesco
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Received on Thu Jun 06 2013 - 00:30:03 PDT
