[gmx-users] Zinc-coordinated protein simulation

Linda fuwei at adrik.bchs.uh.edu
Thu Aug 18 18:02:13 CEST 2005

Hi, David,

    You mean, constrait the distance between Zn and the nitrogen of His/Cys? Am I right? Thanks.


      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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