On Fri, Oct 25, 2024, Maciej Spiegel via AMBER wrote:
>
>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”.
It is recommended to start from standard Amber force fields, and use those
atom types as much as possible. Charges for the modifications should
probably use RESP charges with HF/6-31G*; you probably want to make as many
atoms have charges from the standard force field as possible -- i.e. limit
the number of atoms that have modified charges.
Be sure to check the literature for work similar to what you want to do.
The contributed parameters web page
(
https://ambermd.org/AmberModels_contrib.php) has pointers for how to carry
out RESP calculations, as well as pointers to a variety of modified
nucleotides.
>, 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?
HF/6-31G(d) should only be used for charge determination. Better QM is
appropriate for getting bond, angle and torsion parametes.
>
>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?
Yes, this can often work. Use your chemical intution, and be sure to test
new parameterizations on small systems first, before inserting them into
large nucleic acid constructs.
...good luck...dac
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Received on Thu Oct 31 2024 - 08:00:02 PDT
