[gmx-users] zinc fingers

[Maik Goette]

Hi...
Search the literature for bonded model...I assume you try to simulate 
zif268...?
In that case, zinc is not important for direct binding interactions...so 
the bonded model is quite fine.
For parameters, there is also a bit literature, but if you are able to 
do QM, that would be the best way...
Nevertheless non-bonded and dummy atom method are also described in the 
literature, but didn't work for me.

If you try to model the system with the new OPLSAA-FF Parameters, please 
be aware of these ...they are still under development, and may lead to 
questionable results, altopugh the complex is stable.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Maximiliano Figueroa wrote:
> Hi. I want to simulate a protein with zinc finger complex with DNA (in
> OPLS). My problem is that the zinc atom fly away from the strucutre,
> and I need to keep this atoms in its position (position of
> coordination) How I can do it?
> 
> Thanks, Max
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