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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Received on Tue Mar 04 2014 - 14:00:04 PST
