Re: AMBER: Pang-model of Zn2+

From: Kennie Merz <>
Date: Fri, 26 Mar 2004 08:52:43 -0500

  Non-bonded metal ion models work best in situations where the metal
ion has its coordination requirements saturated. If you have a metal
ion that does not have all of the possible ligand sites occupied (in
Zn+2 this would be five or six) nearby polar groups tend to migrate
into the coordination sphere to satisfy electrostatic requirements.
This then destroys the metal ion site structure, etc. Another point
about the non-bonded models is the need to use an infinite cutoff for
the metal ion center. Maybe this would fix your problem. More details
on this aspect can be found in an article by Stote and Karplus in
Proteins a few years ago now. You could also go the QM/MM route on the
metal center which gives you the best of all worlds - a stable metal
center with dynamics! Good luck. Kennie

On Mar 25, 2004, at 8:44 PM, Peter Oelschlaeger wrote:

> Dear Oliver,
> I have had very good experiences with the "Pang-model". I used it for
> a binuclear metallo-beta-lactamase (Protein Eng. 2003 May;16(5):341-50
> and Biochemistry. 2003 Aug 5;42(30):8945-56).
> It always depends on what you want: if you just want a stable zinc
> binding site, you will be happy with a bonded approach like Ken Merz'
> group uses it. In our case, we explicitely wanted to look at dynamics
> and sensitivy of the active site and allow breakdown of the
> zinc-ligand interactions. Therefore the Pang-model is ideal in MD
> simulations.
> About the fusion of your hydroxide ion to the dummy ion: I thought
> that was ruled out by the van der Waals radius of the central zinc
> atom which extends beyond the dummy atom radii (r = 3.1 , e = 1E-6
> kcal/mol). Maybe you should check on that. In general, we always
> constrain the zinc-dummy molecules during minimization and heating and
> then gradually release the constraints at the simulation temperature.
> In your case it might make sense to do that for the hydroxide, as
> well.
> Hope this helps. Let me know if I can be of further assistance.
> Best regards,
> Peter
> Oliver Hucke wrote:
> Dear All,
> I am wondering if people out there have experience with the Pang
> approach to modeling Zn2+ in proteins?
> I am using the tetrahedral divalent cation approach of Pang, i.e. the
> 2 positive charges are distributed on 4 dummy atoms at the apices of a
> tetrahedron around the Zn. (Prot. Science, v9, pp. 1857)
> One of the ligands of the zinc is a hydroxyl ion. During the
> minimization of my system this ion fuses with one of the dummy atoms,
> which leads to infinite electrostatic energy.
> The fusion seems to happen because the dummy atom has no repulsive
> van der Waals properties (r=0) while its distance to the zinc is
> flexible (force constant = 540). It moves from its equilibrium
> distance from the Zn (0.9A) to a distance close to the r-value of the
> oxygen (1.7A). This comes with a penalty in bond energy dummy-zinc but
> the electrostatics overcome this barrier.
> Has anybody encountered similar problems with this Zn2+ model?
> What is the reasonable behind a flexible zinc dummy distance? Would
> it not be better to fix this distance?
> Best regards,
> Oliver
> --
> **************************************************
> Peter Oelschlaeger, Ph.D.
> Mayo lab, Division of Biology, Caltech
> 1200 E. California Blvd., mail code 114-96
> Pasadena, CA 91125-9600
> Phone: (626) 395-8085, Lab: (626) 395-6407
> Fax: (626) 440-7231
> Email:
> **************************************************
Professor Kenneth M. Merz, Jr.
152 Davey Laboratory
Department of Chemistry
The Pennsylvania State University
University Park, Pennsylvania 16802

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Received on Fri Mar 26 2004 - 14:53:00 PST
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