Hi Jean-Peul,
The 12-6-4 model has been added to Amber 14 as a new feature which will be
released in the coming April. For the Fe3+ ion, the 12-6-4 parameterization
work is undergoing in our group. Since there are also other projects
undergoing, it may take some time for us to get it (and if you are
interested in, we can send you the parameter after we get it). Hope this
helps, if you have more questions or concerns, please tell me.
All the best,
Pengfei
2014-03-05 16:11 GMT-05:00 Jean-Paul Becker <jpb.q4md-forcefieldtools.org>:
>
>
> ----- Message transféré de jean-paul.becker.u-picardie.fr -----
> Date : Wed, 05 Mar 2014 20:32:24 +0100
> De : Jean-Paul Becker <jean-paul.becker.u-picardie.fr>
> Objet : Re: [AMBER] non-bonded parameters for ferric iron and ferrous
> iron
> À : AMBER Mailing List <amber.ambermd.org>, Ken Merz <
> kmerz1.gmail.com>
> Cc : Pengfei Li <ldsoar1990.gmail.com>
>
> Hi Kennie,
>
> Thanks for the answer.
> Regarding the topology of the bonded model we took advantage of our
> RED server and especialy its new version written in Python.
> However, I would be very curions and interested to use your LJ params
> for trivalent cations (ferric iron) on our model and évaluate how they
> perform.
> Right now, I am not sure which way to proceed, I don't know how much
> it implies
> to use 12-6-4 model within Amber.
> Cheers.
> JPB
>
> Ken Merz <kmerz1.gmail.com> a écrit :
>
> > Hi,
> > We created LJ params for the ferrous iron, but not ferric
> > (http://pubs.acs.org/doi/abs/10.1021/ct400146w and
> >
> http://pubs.acs.org/doi/abs/10.1021/ct400751u?prevSearch=pengfei%2Bli&searchHistoryKey=).
> We might be willing to create these for you if you are dissatisfied with
> what is out there. We can create a 12-6 or a 12-6-4 model depending on how
> you want to proceed. To create a bonded model for the coordination
> environment you can use MCPB. Good luck,
> > Kennie
> >
> > On Mar 4, 2014, at 12:08 PM, Jean-Paul Becker
> > <jpb.q4md-forcefieldtools.org> wrote:
> >
> >> Dear Amber users,
> >>
> >> I searched the bibbliography for non-bonded parameters for
> >> a five-coordinate ferric iron.
> >>
> >> There are the well known values coming from D.A. Giammona's PhD
> >> thesis (1.2 and 0.05)
> >> that were once in the Amber contrib but removed recently.
> >> These values are said to be appropriate for a six-coordinate iron
> though.
> >>
> >> In the supporting information of Shahrokh et al. (J. Comput. Chem.
> >> 33:119-133,2012)
> >> one can find three sets of non-bonded parameters either for ferrous
> iron or
> >> ferric iron in different environment:
> >> 1.8 0.01
> >> 1.3 0.002
> >> 1.3 0.01
> >> but reading the paper, the method used to derive these parameters does
> >> not appear clearly.
> >>
> >> In Shahrokh et al., a reference leads to Moore et al.
> >> (Biochemistry 49:9011-9019,1010) where one can read:
> >> "The van der Waals parameters for the heme iron atom were manually
> >> assigne Rii
> >> and epsii values of 1.3 and 0.01, respectively."...
> >>
> >> I am wondering where to look for published and trustworthy non-bonded
> >> parameteres suitable
> >> to ferric iron in a five-coordinate environment.
> >> My question is also more general and applies to ferrous and ferric
> >> iron in five-coodinate
> >> and six-coordinates environmants as well.
> >> Any suggestion would be deeply appreciated.
> >>
> >> Cheers.
> >> JPB.
> >>
> >> --
> >> Jean-Paul Becker
> >> Equipe THERA
> >> Laboratoire des Glucides
> >> FRE 3517
> >> 1 rue des Louvels
> >> 80036 Amiens Cedex
> >> France
> >>
> >>
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> >
> >
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> >
>
>
>
>
>
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--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Wed Mar 05 2014 - 14:00:03 PST
