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

From: Nada Afiva <>
Date: Mon, 21 Sep 2020 19:45:28 +0700

Dear Dac,
Thanks so much for your answer.
The ELE energy term was -9.1259 kcal/mol for ATP system with charge 0, and
it is +47.6188 kcal/mol
for the same system with charge -4. I attach the binding energy files for
both systems.
In my system, the ATP was coordinated with one Mn2+ ion and both systems
contain the same RNA chain.

Please give me more advice in this regard.
Thank you.

Pada tanggal Sen, 21 Sep 2020 pukul 19.14 David A Case <> menulis:

> 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
> simulation.
> ....dac
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Received on Mon Sep 21 2020 - 06:00:05 PDT
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