AMBER Archive (2007)

Subject: AMBER: bound magnesium ions in proteins with GBSA

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Wed Jul 18 2007 - 11:01:26 CDT

Dear Amber users,

I am running a GBSA MD simulation for a metal-protein that has bound
magnesium ions. I am not sure how to deal with bound magnesium ions with
GBSA. I read Tsui&Case's paper in JPC. B 2001, where they used cobalt
hexammine to model fully hydrated magnesium. However, they did free energy
calculation but not GBSA MD. Because bound magnesium ions in proteins are
not fully hydrated, I think it is not suitable to use cobalt hexammine in
metal-protein cases. Does anybody have experience and ideas to deal with
bound magnesium ions in protein when run GBSA MD simulations?

Thank you!

Wei Chen

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