AMBER Archive (2007)

Subject: AMBER: metal ions

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Tue Jun 12 2007 - 16:20:26 CDT

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.

Thanks,

Wei Chen

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu