[gmx-users] Zinc (Zn) parameters

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 17 13:53:42 CEST 2008

Hi Ramon,

Zinc should be considered as one of those "exotic species"
(http://wiki.gromacs.org/index.php/Exotic_Species). It's almost
impossible to give a set of parameters which will work for all zinc
binding sites. Actually, it's best to parameterize based on the
environment. Now, if you have QM/MM calculations, I think it should be
possible to use these to fit parameters.
As for the literature, I believe I had some references to zinc
parameterization in our Proteins paper (TRAIL-DR5 complex) from
earlier this year.

Hope it helps,


On Thu, Jul 17, 2008 at 12:15 PM, Ramon Crehuet <rcsqtc at iiqab.csic.es> wrote:
> Dear Gromacs users,
> I am planing to do MD of an enzyme that has a Zn in its active site. Up
> to now I have used QM/MM or ONIOM approaches but now I need to perform a
> long MD and would like to model the Zn with MM, preferably in OPLS.
> I know that there are three possible approaches: Bonded, nonbonded and
> cationic dummy atom. I have seen a thread, where Maik Goette said that
> onyl the bonded approach worked. I would like to know in more detail
> what kind of problems could I encounter. What does "not work" imply?
> Weeks of unreliable calculations...?
> I would also be very grateful if people working in this area could send
> me some reference publications, in particular of what can be done with
> Gromacs. I have only found: "Zinc binding in proteins and solution: A
> simple but accurate nonbonded representation" Roland H. Stote, Martin
> Karplus, 1995.
> Thanks in advance,
> Ramon
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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