Re: [AMBER] mmgbsa question

From: David A Case <>
Date: Tue, 16 Jun 2020 08:02:35 -0400

On Tue, Jun 16, 2020, MYRIAN TORRES RICO wrote:
>I have a question about the several methods in MMGBSA calculations. I
>have carried out MD of 125ns in complexes carbohydrate-protein, and
>next I launched over my outputs mdcrd.files MMPBSA and MMGBSA
>calculations. I have read that depending the raddi bond (mbondi,
>mbondi2...) the igb is different. I have used GB-OBC2 (igb=5) and I
>think that it corresponding to mbondi2, but...what does it depend on
>that you use igb=1, 2 or whatever?

Please see Chapter 4 in the Reference Manual, which describes the
various types of gb supported with Amber. Table 4.1 shows the radii
that are recommended for each variant.

I'm not sure I'm answering your question, though. You might want to
look at papers that carry out similar calculations, or consult a recent

%A E. Wang
%A H. Sun
%A J. Wang
%A Z. Wang
%A H. Liu
%A J.Z.H. Zhang
%A T. Hou
%T End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
%J Chem. Rev.
%V 119
%P 9478-9508
%D 2019

...good luck....dac

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Received on Tue Jun 16 2020 - 05:30:03 PDT
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