Hi Maciej,
.. you can find some info and additional tips for possible ff combinations in our recent paper: https://pubs.acs.org/doi/10.1021/acs.jctc.4c00601
In the paper, we tested performance of popular DNA and RNA ff combinations and identified certain issues that you may encounter in your project.
Good luck!
Vojtech.
On 15. 10. 2024, at 8:41 PM, Maciej Spiegel via AMBER <amber.ambermd.org> wrote:
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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Vojtech Mlynsky
Structure and Dynamics of Nucleic Acids
Institute of Biophysics of the Czech Academy of Sciences
Kralovopolska 135, 612 00, Brno, Czech Republic
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Received on Wed Oct 16 2024 - 02:30:04 PDT
