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.
Good luck,
Ross
> -----Original Message-----
> From: Manish Datt [mailto:manish.datt.hotmail.com]
> Sent: Monday, April 18, 2011 7:43 AM
> To: amber.ambermd.org
> Subject: [AMBER] FW: Leap error with Zinc ions
>
>
> Hi All,
>
> Last week I sent the question below but got no reply. So I'm asking a
> rather general question.
> What is the best way to run simulation of a protein having Zinc ions
> coordinated to CYS and HIS resiudes?
> Any pointers to the parameters would be helpful.
>
> Thanks,
>
> Manish
>
>
> From: manish.datt.hotmail.com
> To: amber.ambermd.org
> Subject: Leap error with Zinc ions
> Date: Thu, 14 Apr 2011 10:22:29 -0400
>
>
>
>
> Hi All,
>
>
> I trying to prepare a system with protein having tetrahedrally
> coordinated zinc ions. I using the cationic dummy atom approach. But I
> getting following error in Leap:
>
> ERROR: Comparing atoms
> .R<CYM 261>.A<SG 8>,
> .R<CYM 263>.A<SG 8>,
> .R<CYM 264>.A<SG 8>, and
> .R<CYM 265>.A<SG 8>
> to atoms
> .R<ZNB 270>.A<D2 3>,
> .R<ZNB 270>.A<D1 2>,
> .R<ZNB 270>.A<D3 4>, and
> .R<CYM 261>.A<SG 8>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 140
> !FATAL: Message: Atom named D2 from ZNB did not match !
> !
> !ABORTING.
>
>
>
> Complete Leap log and pdb files are attached
>
> Please help me solve this problem.
>
>
> Thanks,
>
>
> Manish
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Received on Mon Apr 18 2011 - 09:30:04 PDT
