AMBER Archive (2007)

Subject: AMBER: Metal ions in GBSA

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Tue Jun 12 2007 - 08:13:36 CDT

Dear Amber users,

I am running an implicit MD with GBSA. My system is a metal-protein. During
simulations, metal ions diffuse away quickly. I am thinking it is because of
the absence of the first shell of water. The simplest way to keep metal ions
is to put some restraints. Does anybody has better ideas to keep metal ions
in proteins or recommend a reference?

Thanks a lot!

Wei Chen

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