[gmx-users] Zinc-coordinated protein simulation

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Aug 19 15:01:34 CEST 2005

The method, David mentioned is a third possibility.
It depends, what goal you want to achieve.
If the Zinc is complexed and "just" important to stabilize your
structure, the bonded method also works.
The problem with that method is, that, as I know, no parameters are
I took the mean of the distances in the crystal structure as bond length
and a weak force constant, which I took by intuition...:). I did the
same for the angles. I think, you don't have to care about the
dihedrals...It worked fine with no settings (so GROMACS sets 0s, when I
remember correctly).
The charge on the zinc shouldn't be 2, according to severeal papers,
which used that method. with a charge of around .7 it worked fine. Don't
forget to spread the opposing charges equally to the 4 complexing atoms,
to achieve a 0 total charge.
If your zinc has a catalytical function, you should try the dummy
method. This never worked for me, but as I now know, I made fatal
mistakes in configuring it. So just give it a try...I will do that in
the future again, but at the moment, this has no priority.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Linda wrote:
> Dear gmx user,
>     I just searched gmx mailing list about the zinc-coordinated enzyme simulation, it seems that most people encouter the problem that the zinc goes away from coordinated residue (Cys/His) in enzyme. I saw some people tried to solve this problem with two methods: 1. cationic dummy atom method. 2. bonded zinc with His or Cys. I wonder someone has succeeded? If so, would you please share your experience? Thanks.
> Cheers,
> Linda
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