[gmx-users] Zinc-coordinated protein simulation

David spoel at xray.bmc.uu.se
Tue Aug 16 20:52:07 CEST 2005

On Tue, 2005-08-16 at 12:08 -0600, 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.

We've done it with distance restraints. Check
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, 551-565, 2003

> Cheers,
> Linda
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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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