Re: [AMBER] reg-Generalized Born Approach

From: case <>
Date: Thu, 1 Apr 2010 08:12:03 -0400

On Thu, Apr 01, 2010, maya maya wrote:
> Why one should not use the value igb=2 for the DNA , if they do so what will
> be the problem with the dynamics.

I don't think anyone knows, since most published studies of DNA duplex
dynamics using Amber GB have used igb=1. (I may have missed some studies.)
You might find it of interest to explore this issue. But DNA in our implicit
solvent models is near the limit of melting, and you should be aware that
changes in the solvent models may yield unpredictable results. Same comments
apply concerning gbsa.


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Received on Thu Apr 01 2010 - 05:30:04 PDT
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