Re: [AMBER] MMGBSA energy calculation problem for RNA

From: Liao <>
Date: Wed, 25 Sep 2019 23:18:38 +0800

Thanks there Professor Case,

As I found out that igb=5 and igb=8 made a huge difference, though I’m yet to find out why.
Yes doing it by hand is essential, though I still need to figure out sander’s commands’ compatibility between old and new Amber-some of them seem to be incompatible, at least from my preliminary try. Still checking Amber 19’s manual for the newest by-hand MMGBSA examples.

> On Sep 25, 2019, at 9:54 PM, David Case <> wrote:
>> 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 - 08:30:03 PDT
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