[AMBER] MMGBSA energy calculation problem for RNA

From: Liao <liaojunzhuo.aliyun.com>
Date: Wed, 25 Sep 2019 18:49:23 +0800

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?


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Received on Wed Sep 25 2019 - 04:00:02 PDT
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