AMBER: metal ions

From: Wei Chen <>
Date: Tue, 12 Jun 2007 17:20:26 -0400

Hello, Amber users,

As I posted early, I used GBSA to simulate a protein binding with metal ions
(magnesium). The metal ions coordinate with oxygen atoms in side chains. But
the metal ions just jump out from binding sites right away when I reduce
restraint from 1kcal/mol to 0.1 kcal/mol. It seems that it is unfavorable to
stay in binding sites with GBSA. However, the metal ions did stay in binding
sites with explicit water simulations. So I am wondering if anything is
wrong with GBSA or it has some limitation in this case.


Wei Chen

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Received on Wed Jun 13 2007 - 06:07:36 PDT
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