Re: [AMBER] MMPBSA binding energy was positive for charged ligand

From: David A Case <>
Date: Mon, 21 Sep 2020 08:14:23 -0400

On Mon, Sep 21, 2020, Nada Afiva wrote:
>I was preparing a system for ATP complexed with RNA and protein using
>AM1-BCC charge, then performed 100 ns MD simulation and calculating the
>MM-PBSA binding energy.
>If I used the charge for ATP=0 in the preparation step, then the MMPBSA
>final binding energy was around -30 kcal/mol, however when I used the
>charge for ATP=-4, then MMPBSA final binding energy become positive.
>All other parameter was the same in both systems.

You should confirm that the difference is in the electrostatic
component. However, ATP is *very* often coordinated with one or more
Mg2+ ions, and so doesn't really carry a -4 charge. If you have RNA
around, there might be enough non-neutralized negative charge to repel
the ATP. Anyway, that's something to think about, and to check in the


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Received on Mon Sep 21 2020 - 05:30:02 PDT
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