Re: [AMBER] MMGBSA energy calculation problem for RNA

From: David Case <>
Date: Wed, 25 Sep 2019 13:54:17 +0000

On Wed, Sep 25, 2019, Liao wrote:

>The issue is that I’ve ran the exact same molecule before with AMBER11,
>and the binding energy result was very reasonable, at -71 kcal/mol. The
>only significant system setup difference I can think of is that back with
>AMBER 11 there was no charge neutralization via Tleap with Na+ for the
>solvated complex, and now with AMBER 19 22 Na+ were added to neutralize
>the system.

The way to proceed here is to run MM-PBSA "by hand" so that you know
exactly how things like ions are being handled. (See the coments at the
beginning of Chap. 32 in the Reference Manual.)

The "classic" implicit solvent approach is to consider mobile ions like
Na+ as the part of the solvent, that is, to strip then out before doing
any analysis. It's not clear (to me) how well alternative approaches
that try to treat ions as a part of the RNA may be expected to work.
Nor do I know (although others on this list may know) how various
automated scripts between Amber11 and Amber19 might have handled this.
Hence the recommendation to make sure you understand in detail exactly
what the automated scripts are going.

>From the current energy results, the G for the gas phase dsRNA complex
>seems to be quite high (compared to the 2 single strands) like as if the
>negative charges on RNA are repulsing the 2 strands away.

This is exactly what I would expect to be happening. Solvent screening
(from both dielectric effects and from mobile counterions) will
mostly cancel this electrostatic repulsion.

....good luck....dac

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Received on Wed Sep 25 2019 - 07:00:02 PDT
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