Hi,
the first workaround is using charmm forcefield.....
The second is the answer given by in
http://archive.ambermd.org/201205/0522.html
where is stated: there is no "CHARMM way" or "AMBER way" to parametrize
such exotic molecules
Anyway, recently in this paper
http://pubs.acs.org/doi/abs/10.1021/ct300185u
new parameters, amber compatible, regarding FeS cluster had been published.
Francesco
2012/5/25 Wilson, Katie <ka.wilson.uleth.ca>
> Hi,
> What is required to use CHARMM parameters in AMBER? I have parameters for
> everything but the Fe:S cluster and would only need the CHARMM parameters
> for the Fe:S cluster.
> Thanks,
> Katie
>
> > Hi,
> > maybe this paper is interesting for your purpose:
> > http://dx.doi.org/10.1021/bi200046p
> > Actually, they develop parameters for CHARMM (that can be used with the
> > AMBER program),
> > anyway as stated anyway in this mailing list, there is no "CHARMM way" or
> > "AMBER way"
> > to parametrize such exotic molecules,
> >
> > Regards,
> > Francesco
> >
> > 2012/5/17 Wilson, Katie <ka.wilson.uleth.ca>
> >
> >> Hi,
> >>
> >> I am trying to set up my calculation for a DNA protein complex and there
> >> is a 4Fe:4S cluster in the protein. Are there parameters for 4Fe:4S
> >> clusters to use in AMBER or a way to parametrize the 4Fe:4S cluster for
> >> use in AMBER?
> >>
> >> Thanks,
> >> Katie
> >>
> >>
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> >>
> >
> >
> >
> > --
> > Cordiali saluti, Dr.Oteri Francesco
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> >
>
>
>
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--
Cordiali saluti, Dr.Oteri Francesco
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Received on Fri May 25 2012 - 10:00:03 PDT
