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

From: neildancer <>
Date: Tue, 22 Sep 2020 21:11:08 +0800

   Hi Nada
     I tried to prepare ATP molecule before, such as charge calculation,
   topology build via GAFF and tleap. But, during the md stage, the ATP
   molecule always had blowing up errors, because the hydrogen atom of ATP
   showed some unusual things. So could you describe some details about ATP
   preparation, and how do you add the hydrogen atoms to ATP? Thank you!
   Best wish
   Ning Wang

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   On 09/21/2020 20:45, [2]Nada Afiva wrote:

     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 Tue Sep 22 2020 - 06:30:03 PDT
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