Dear Ross,
Thanks for your instant reply.i really seached the Mailing List and consulted the related papers.Yes, there are a lot of related papers,but i cannot found i wanted, and i hope someone who had done the same system as i am working on and could give me the related parameters. Because i found it is a time consuming and rather advanced work to develop it myself.May be you are right. If i cannot find the parameters i have to do it on my own.
Best regards!
kk zhu
> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
> Date: Fri, 16 Sep 2011 09:18:15 -0700
> Subject: Re: [AMBER] help ! zinc parameters
>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Sep 19 2011 - 05:30:03 PDT
