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

From: Swagata Halder <swagatah.iisc.ac.in>
Date: Fri, 4 Oct 2019 06:20:45 +0000

HI,

Thanks for your quick reply. My expectations for GC/GC step and AU/AU step are near about -14 Kcal/mol and -9Kcal/mol respectively. Stacking energies which I got from pair wise analysis are higher compared to other standard reference values ( Daniel et al. Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps
in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations? J. Phys. Chem. B 2010, 114, 11911203). Yes, I am using canonical tetraloop structure.


Regards,
Swagata Halder
Indian Institute of Science.



________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Thursday, October 3, 2019 2:39 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop

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

Bill

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 - 23:30:03 PDT
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