Hi Manish,
On 18/4/2011, at 12:10 p.m., Ross Walker wrote:
> Hi Manish,
>
> I suggest reading the papers by Ulf Ryde where he calculates parameters for
> zinc, specifically bound to Cysteine and Histidine. I would also do a
> citation check on these papers to see if there are newer zinc parameters
> that cite these.
>
> Ryde, U. Proteins: Struct., Funct., Genet. 1995, 21, 40.
> Ryde, U. Eur. Biophys. J. Biophys. Lett. 1996, 24, 213.
> Ryde, U. J. Comput.-Aided Mol. Des. 1996, 10, 153.
>
> You can also check my PhD thesis here:
>
> http://www.rosswalker.co.uk/files/Ross_Walker_Thesis_Final.pdf
>
> And also the following two publications:
>
> Walker, R.C., Klug, D.R. et al. "Large and fast relaxations inside a
> protein: Calculation and measurement of reorganisation energies in alcohol
> dehydrogenase.", J. Phys. Chem. B., 2002, 106(46). 11658-11665
>
> Walker, R.C., Cho, B.M., Amer, H., Mercer, I.P., Gould, I.R., Klug, D.R.,
> "The effect of adiabaticity on electron dynamics in Zinc Myoglobin." J.
> Phys. Chem. B., 2005, 109(12), 5954-5961.
If you need different parameters to those in the references Ross gives, you could also try MCPB, which is included in the recently-released AmberTools 1.5. MCPB was used to develop the ZAFF force field, which is described in this paper:
http://pubs.acs.org/doi/abs/10.1021/ct1002626
Hope that helps,
Ben
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Received on Mon Apr 18 2011 - 10:00:04 PDT
