[gmx-users] Modeling Zinc in OPLS

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 2 12:10:25 CET 2005

On Wed, 2005-03-02 at 09:43 +0100, Maik Goette wrote:
> Hi
> 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)

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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