Re: AMBER: Minimisation and heating under GB conditions

From: David A. Case <>
Date: Mon, 3 Nov 2008 09:01:59 -0500

On Mon, Nov 03, 2008, Carlos Simmerling wrote:
> also I STRONGLY recommend against igb=1. we've published several
> papers (as have others) showing that this is not a good option. I
> recommend igb=5 and mbondi2 radii.

Just a (somewhat off-topic) note: the comments above are based on studies on
proteins. For nucleic acids, we have less extensive study, but igb=1 is
likely to still be a viable option there.


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Received on Fri Dec 05 2008 - 10:30:49 PST
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