Il 29/10/2011 16:27, case ha scritto:
> 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.
I believe mixing different force-fields is not a good practice
>
>> 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:
I found parameters for the Fe4S4 on (Chang et. al, 2004;
http://dx.doi.org/10.1021/ct800342w)
and for the Fe3S4 on (Meuwly et al., 2003;
http://dx.doi.org/10.1039/b211407k).
In these papers the BLYP/6-13+G* and the UBLYP/6-31+G* approaches are
used. Are them suitable for AMBER
force field?
Anyway I sent an e-mail to prof. Toshiko Ichye to obtain her parameter
set for the cubane iron-sulphur cluster
>
> 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 am reading this paper, I think I would use it as a template to derive
charge for my system.
Is the
>
> 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
I guess the parameters you are talking about are not yet ready for the
MD simulation, is it right?
>
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Received on Sat Oct 29 2011 - 14:00:03 PDT
