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

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From: Swagata Halder <swagatah.iisc.ac.in>
Date: Thu, 3 Oct 2019 07:58:58 +0000

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 - 01:00:02 PDT