[gmx-users] Zinc-coordinated protein simulation

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 18 17:14:19 CEST 2005

On Thu, 2005-08-18 at 10:02 -0600, Linda wrote:
> Hi, David,
>     You mean, constrait the distance between Zn and the nitrogen of His/Cys? Am I right? Thanks.
No, *restrain* the distance between His-NE or Cys-SG and Zn.

> Linda
>       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
> Best regards, 
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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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