Re: [AMBER] MMGBSA on Protein-DNA/RNA complex

From: Vlad Cojocaru <>
Date: Tue, 23 Jun 2015 13:32:42 +0200

We had quite poor experiences with MMGBSA for protein-nucleic acids interactions not only because we got completely unrealistic absolute binding free energies but also because of rather poor agreement with experiment of relative dGs. Therefore, we use MMPBSA.

For the protocol we use see the paper by Merino et al. in Structure 2014 (Structural basis for the SOX dependent redistribution of OCT4 ...) . Although in the paper we focus mostly on DNA-mediated protein-protein interactions, we did play with the protocol to optimize as much as possible the protein-DNA energies.

A word of caution: multiple tests with the PBSA parameters beyond those specified via is required.

We are also preparing a follow up study with more discussion on the influence of the PBSA parameters on the results.

Hope this helps

On June 23, 2015 12:32:15 PM CEST, Muthukumaran R <> wrote:
>Dear amber users,
>I found from literature and mailing list that implicit simulations for
>nucleic acids is not properly parameterized. I have done explicit
>simulations for protein-DNA and protein-RNA complexes. I want to study
>specificity of protien towards DNA/RNA, in this regard I have performed
>binding energy calculations using mmgbsa (AMBER 12 and Amber tools 13)
>Input used:
> &general
> startframe=20000, endframe=25000,interval=50,
> verbose=2, keep_files=1,
> /
> &gb
> igb=5,
>1. is it possible to study specificity using MM-GBSA.
>2. As it is a relative method, is it meaningful to compare the binding
>energies of DNA and RNA?
>3. In regard to the gb model, I have adopted igb=5 (modified OBC model)
>used in "A Computational Study of Nucleosomal DNA Flexibility by Jory
>Ruscio and Alexey Onufriev". is this still an accepted model for
>nucleic acids.
>Apart from MM-GBSA, is there any other analysis/method for studying the
>specificity of Protein towards DNA and RNA.??
>AMBER mailing list

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Received on Tue Jun 23 2015 - 05:00:02 PDT
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