Update:
So after trying countless different things, somehow when I changed the igb=8 to 5, to be the same as with in my AMBER 11, the energy looked correct again, approx. -70 kcal/mol for a 9 residue long dsRNA.
Hope this also helps someone.
> On Sep 25, 2019, at 6:49 PM, Liao <liaojunzhuo.aliyun.com> wrote:
>
> Dear Users,
>
> Need some help here.
>
> With AMBER19 I’m running MD simulations of a 9-residue long dsRNA, and measuring binding energy of the 2 strands. Everything up to generating the MD trajectory looks perfect.
>
> Problem is, with MMGBSA.py for energy estimations, the binding energy of the 2 strands is erroneously high, at +200 kcal/mol. (The trajectory looks great as it should.)
>
> 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.
>
> 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.
>
> I’m guessing maybe the ions are causing the energy calculations error, but should it?
>
> Thanks!
> James
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Received on Wed Sep 25 2019 - 08:30:02 PDT
