[gmx-users] Modeling Zinc in OPLS

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Mar 3 10:04:31 CET 2005


Without going to deep into the paper, I personally think, distance 
restraining the zinc is a good idea, but I can't see the difference 
between your approach and the bonded approach, if the zinc has "just" a 
structure stabilizing function.


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/

David van der Spoel wrote:
> On Wed, 2005-03-02 at 09:43 +0100, Maik Goette wrote:
>>I also use Zn in my simulations.
>>There are 3 possibilities:
>>Bonded, nonbonded and cationic dummy atom approach.
>>Unfortunatly, nothing except the bonded approach worked for me.
>>If you need help with the bonded approach, tell me.
>>If you are able to work with one of the both nonbonded methods, tell me.
>>What is the job of zinc in your sim?
> Actually we have used distance restraints to keep it in place, see:
> Manzetti et al., Molecular dynamics of MMP-3, ADAM-9 and ADAM-10 in
> complex with hypothetical substrates: New implications for catalysis and
> substrate affinity J. Comp. Aid. Mol. Des. 17 pp. 551-565 (2003)

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