Dear Ben,
Thank you very much.
I also need this information.
regards
setyanto
On Mon, Apr 18, 2011 at 11:42 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> 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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>
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Received on Tue Apr 19 2011 - 06:30:09 PDT
