This nay be useful
https://pubs.acs.org/doi/10.1021/acs.jctc.4c01164
On Thu, Oct 31, 2024, 1:47 PM Maciej Spiegel via AMBER <amber.ambermd.org>
wrote:
> Thank you for your response.
>
> > HF/6-31G(d) should only be used for charge determination. Better QM is
> > appropriate for getting bond, angle and torsion parametes.
>
>
> Therefore, I can optimize the structure at PBE0-D4/def2-TZVP (+SMD
> solvent) and then use this optimized structure to derive charges with
> HF/6-31G(d), correct?
>
> Regarding missing parameters in AMBER, is it acceptable to, for example,
> run:
> parmchk2 -i FDY.mol2 -f mol2 -o FDY_missing.frcmod -s parm10
> parmchk2 -i FDY.mol2 -f mol2 -o gaff2.frcmod -s gaff2
> and replace the “ATTN, needs revision” entries in FDY_missing.frcmod with
> the corresponding entries from gaff2.frcmod?
>
> best
> –
> 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
>
> > Wiadomość napisana przez David A Case <dacase1.gmail.com> w dniu
> 31.10.2024, o godz. 15:53:
> >
> > 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
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 02 2024 - 14:00:02 PDT
