Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop

From: Bill Ross <>
Date: Thu, 3 Oct 2019 02:09:12 -0700

What are your expectations, and what are they based on? Are you using a
canonical tetraloop structure?


On 10/3/19 12:58 AM, Swagata Halder wrote:
> Hi all,
> I am calculating stacking energy of a RNA containing UUCG tetraloop by cpptraj pair wise command (Amber 18). Unfortunately I got some higher value than expected. As a example for GC/GC step I got -40Kcal/mol and for AU/AU step , got -35Kcal/mol. Please suggest me if anything is going wrong for the calculation.
> Thanks in advance.
> Regards,
> Swagata Halder
> Indian Institute of Science
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Received on Thu Oct 03 2019 - 02:30:02 PDT
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