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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 25 2024 - 09:30:01 PDT
