Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model]

From: David A Case <>
Date: Wed, 31 Jul 2013 07:43:13 -0400

On Wed, Jul 31, 2013, Catein Catherine wrote:

> However, it is not clear to me the differences between igb=2 or igb=5.

Join the club! I don't think there are any systematic diffs between these two
models. And both are now obsolete. For proteins, my recommendation is to use
igb=8; for nucleic acids, I personally still like igb=1, but opinions differ.
See, e.g.

%A T. Gaillard
%A D.A. Case
%T Evaluation of DNA Force Fields in Implicit Solvation
%J J. Chem. Theory Comput.
%V 7
%P 3181-3198
%D 2011


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Received on Wed Jul 31 2013 - 05:00:03 PDT
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