[AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21)

From: Maciej Spiegel via AMBER <amber.ambermd.org>
Date: Fri, 25 Oct 2024 18:28:36 +0200

Dear Users,

I am new to molecular dynamics and am currently working on modified DNA/RNA nucleosides, derived from the OL21 and OL15 available templates, respectively. I would like to stick with these force fields instead of GAFF2, but I am wondering if it's reasonable to use GAFF2-generated parameters if the DNA/RNA forcefields cannot find them and yield “ATTN, needs revision”.

Alternatively —and maybe that’s even more wise — I could derive parameters using QM calculations. OL21 seems to be primarily based on parm99 (Figure 1 of https://doi.org/10.1021/acs.jctc.3c00233 <https://doi.org/10.1021/acs.jctc.3c00233>). According to the Amber24 manual and related studies:
- https://doi.org/10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F <https://doi.org/10.1002/1096-987X(200009)21:12%3C1049::AID-JCC3%3E3.0.CO;2-F>
- https://doi.org/10.1002/jcc.540161106 <https://doi.org/10.1002/jcc.540161106>
- https://doi.org/10.1021/ct600329w <https://doi.org/10.1021/ct600329w>
, it seems that HF/6-31G(d) was used. I must not use a higher-level quantum theory, such as PBE0-D4/def2-TZVP for scans and fitting, as it might introduce inconsistencies. Is my understanding correct?

Finally, can the DU atom of "antechamber […] -at AMBER” type be simply resolved by manually editing it in the RESP-fitted .mol2 and then providing a .frcmod file encompassing this new atom type during the tleap step?

Thanks in advance,

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 Fri Oct 25 2024 - 09:30:01 PDT
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