On Sat, Oct 29, 2011, Francesco Oteri wrote:
> I have to simulate a protein made by three iron sulphur cluster, namely
> one 4Fe4S, one "canonical" 3Fe4S and one "not-canonical" 3Fe4S.
> The topic of the research is the caracterization of the overall protein
> structure, so I don't need an accurate representation of the clusters.
> Although I found CHARMM parameters for the 4Fe4S and 3Fe3S clusters, I
> prefer using AMBER-ILDN force-field.
I don't see any good reason not to use the CHARMM Fe-S parameters in
conjunction with the Amber protein force fields.
> The problem are atomic charges.
Getting charges for iron-sulfur clusters is tricky, since the irons are
high-spin, and you need to use a broken-symmetry approach to obtain a suitable
wavefunction. I'm not sure what CHARMM parameters you have, but if they came
from Toshiko Ichiye's group, they are probably fine. Some other charge models
are reported here:
R.A. Torres, T. Lovell, L. Noodleman and D.A. Case. Density
functional and reduction potential calculations of Fe4 S4
clusters. J. Am. Chem. Soc. 125, 1923-1936 (2003).
I think you would have to put in a ton of work to come up with charge models
that would be arguably better than the ones mentioned above.
We have a draft paper reporting a full force field for Fe4S4 cubanes, but are
experiencing the usual problems of going from 90% done to 100% done....
...good luck....dac
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Received on Sat Oct 29 2011 - 07:30:03 PDT
