AMBER Archive (2006)

Subject: AMBER: Oon Modeling the metalloprotein with GB model.

From: wenfei Li (wfli_at_biophy.nju.edu.cn)
Date: Mon Sep 11 2006 - 02:41:16 CDT

Dear Amber users,

I'm trying to perform long time-scale simulations to the zinc containing proteins (e.g. zinc fingers). I prefer to use the GB model in dealing with the solvent effect considering the sampling efficiency. However, with the GB model, the effects of the coordination bond formation between the zinc ions and the water molecules can not be described. These zinc-water coordination bonds may affect the formation of other coodination bonds between the zinc ion and residues during folding/unfolding.

Does anyone have any experiences or suggestions on how to model the metalloproteins (coordination bonds) with the GB model (if it is possible)?

Thanks a lot,

Wenfei

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