[gmx-users] Zinc (Zn) parameters

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Jul 25 15:27:45 CEST 2008

Hi Ramon

As Tsjerk already mentioned, its generally not that easy with such an 
"exotic" metal.
Depending on the question you want to get answered, certain aspects 
should be regarded.
If the zinc is just keeping the structure in the correct conformation, 
and is not directly included in the region of interest, the probably 
easiest way is to use the bonded method, where you simply introduce 
bonds, which keep the ZN in place (due to LINCS or SHAKE). A harmonic 
potential didn't work here (for me).
However, if this is not possible because it resides e.g. in a  catalytic 
center of interest, its not that easy.
The cationic dummy method is probably hard to apply, because the 
construction of virtual particles in GROMACS depends on at least two 
real particles. This is obviously not true for one ZN atom.
Therefore, the best you can do is, using Tsjerks hint and compute the 
charge on your ZN in its environment via QM and see, if it remains, 
where it should.
I observed, that ZN likes to leave its place, when complexed to 2 CYS 
and 2 HIS, given a charge of ~ 0.7.

Maybe, also dependent on your interest, QM/MM could help here.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2305
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Ramon Crehuet 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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