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 - 09:30:03 PST
