AMBER Archive (2008)

Subject: Re: AMBER: Minimisation and heating under GB conditions

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Nov 03 2008 - 08:01:59 CST

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.

...dac

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