Hi Maciej,
You would load your hybrid helix in leap after sourcing leaprc.DNA.OL15 and
leaprc.RNA.OL3.
As long as your residue names are correctly labeled (As G/U/A/C for RNA and
DG/DC/DT/DA for DNA) the correct force field will be applied to the DNA and
RNA nucleotides.
You can check this against those force fields by using parmed (check for
the correct atom types for OL15/OL3: eg., C5' is CJ in OL15 and CI in OL3
among other changes)
Others who have more experience with hybrid duplexes may have more/better
advice.
-Christina
On Tue, Oct 15, 2024 at 2:41 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Tue Oct 15 2024 - 12:00:02 PDT
