Dear Amber Users,
I am planning to study RNA-DNA duplexes, and later, I will also investigate modified nucleosides. The question arises: which force field should I use?
I am considering either OL15 or OL3 (specifically RNA.LJbb) and parametrizing either uridine or thymidine, respectively, with the pGM-perm RESP methodology.
What are your thoughts on this approach? Perhaps there’s a more efficient method?
–
Maciej Spiegel, MPharm PhD
assistant professor
.GitHub <
https://farmaceut.github.io/>
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
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Received on Tue Oct 15 2024 - 12:00:02 PDT
