Hi Kyle,
Atom types changes and rationale are given in the ff14sb and ff19sb
papers...
On Thu, Aug 1, 2024, 11:04 AM Warren, Kyle Benjamin via AMBER <
amber.ambermd.org> wrote:
> Hi all,
>
> I'm trying to generate parameters for a modified nucleobase
> (wybutosine-86), and I'm finding it hard to decide on an apt atom type to
> best describe the Nitrogen in the 6 membered ring bound to the hydrogen.
> Per the ff99 paper (I know this one is outdated), this nitrogen atom type
> in a 6 membered ring with a hydrogen is labelled "NA", an "sp2 nitrogen in
> aromatic rings with hydrogen attached (e.g. protonated His, Gua, Trp)".
> Yet, when I refer to the *parm10.dat* file describing ff14SB atom types,
> NA's definition has changed to be "sp2 N in 5 memb.ring w/H atom (HIS)",
> which of course no longer describes my atom in question.
>
> The only other close atom type in the *parm10.dat* file that describes my
> atom in question would be "N*", an "sp2 N", however, this atom type is
> usually reserved for aromatic sp2 Nitrogens bound to 3 carbons as seen in
> the Nitrogen that facilitates the ribose-nucleobase glycosidic linkage, and
> the 5&6 membered ring junction seen in wybutosine (see attached png).
> Additionally, in the ff99 paper, N* is described as being an "sp2 nitrogen
> in 5-membered ring with carbon substituent (in purine nucleosides)" which
> only adds to my confusion.
>
> Should I strictly go by the atom type definitions found in parm10.dat and
> omit the ff99 paper? Despite the definition discrepancies, do these atom
> types have conserved properties between forcefields? Any help would be
> greatly appreciated.
>
> Cheers,
>
> Kyle Warren
>
> ff19 paper I referenced: doi/10.1021/ja00124a002
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Received on Thu Aug 01 2024 - 09:00:02 PDT
