Hi Zhu,
"searched through our Mailing List and consulted the related papers"
Are you really sure you actually did this? - A simple search for Zinc
Parameters on
http://archive.ambermd.org/ turns up a number of useful hits.
I suggest you read through these first since this question has been answered
a number of times on the mailing list. There is are also an extensive number
of manuscripts dealing with the parameterization of Zinc.
You can take a look at the following papers and the references they cite for
the Zinc coordination:
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.
You can also take a look at my Ph.D thesis available here:
http://www.rosswalker.co.uk/reports1.htm
This has a significant amount of discussion on simulating Zinc bound to CYS,
HIS and other molecules in LADH and Zinc-myoglobin.
The parameters here are derived from the following manuscripts:
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 could also consider the ZAFF force field: Peters M.B. et al, J. Chem.
Theory Comput., 2010, 6 (9), pp 2935-2947
A simple search of the literature would have uncovered these works (and
others). I would suggest becoming familiar with how to conduct such searches
and reviews of the literature since it is a critical skill in becoming a
successful scientist.
Good luck,
Ross
> -----Original Message-----
> From: Kk Zhu [mailto:hkhhh.k.163.com]
> Sent: Thursday, September 15, 2011 11:46 PM
> To: amber.ambermd.org
> Subject: [AMBER] help ! zinc parameters
>
> Dear amber users,
>
> There is a troublesome problem which hinder me for a long time and i
> am eager for your kind help.
>
> Two Zinc ions was embedded in the protein which i want to simulate
> with AMBER, the one Zinc ion coordinated with 3 HIS,and the other one
> coordinated with HIS ,CYS ,ASP and a structure water molecule.
>
> Unfortunately, i didn't find the corresponding parameters could be
> used in AMBER for these two protein-metal coordination system after i
> searched through our Mailing List and consulted the related papers. As
> a beginner for AMBER, i have litter idea for how to get or develop
> these parameters properly. So could someone be so kindly to give me
> some helpful guide for this tough problem? Or could someone have the
> similar experience and have developed these parameters could be used in
> AMBER ff?
>
> Any suggestions will be greatly appreciated! Thanks everyone in
> advance!
>
> Best regards!
>
> Kongkai Zhu
>
>
>
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Received on Fri Sep 16 2011 - 09:30:04 PDT
