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From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Fri Apr 08 2022 - 01:29:41 CDT

Sorry for the late reply,

The torsions are topologically separate (unlike phi/psi torsions for which
CMAP was developed), will this not pose any problems? I've tried searching
for the commands to derive the CMAP corrections in the CHARMM documentation
but I don't see anything specifically related to 2D grid corrections. I
don't mind doing some scripting, but I am a complete beginner at CHARMM. Is
this feasible do you think?

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Sat, 28 Aug 2021 at 00:35, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> Hi Daniel,
>
> it's a problem I've seen several times before, and it can happen with
> strongly correlated torsions. The solution we used was to run 2D torsional
> scans and introduce CMAP terms in the force field. That is a more manual
> procedure, which FFTK won't help you with very much.
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002532__;!!DZ3fjg!qB3L05ebwCdz1zE77B-ZWhlJxdTSpIxvoYFjrqfv1MF8CWa6mu9-mY3wb29CFi5XxA$
> details here:
> https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002532.s008__;!!DZ3fjg!qB3L05ebwCdz1zE77B-ZWhlJxdTSpIxvoYFjrqfv1MF8CWa6mu9-mY3wb2_UG90uzA$
>
> Jerome
>
> ----- On Aug 26, 2021, at 5:18 PM, Daniel Fellner <
> dfel694_at_aucklanduni.ac.nz> wrote:
>
> Hi all,
> I'm in the process of optimising the dihedral terms for a particularly
> crowded molecule. The dihedrals in question are between two aryl groups
> connected by a tertiary amide through -N- and I've trimmed excess
> functional groups off to use the bare minimum model compound as a stand-in
> for the full molecule.
>
> Unfortunately, when analysing the scan outputs there are both major and
> minor 'jumps' or discontinuities caused by sudden rotation of one of the
> aryl groups into a more favourable conformation. I'm assuming the larger
> jumps make the PES unsuitable for use, though perhaps those under ~+/- 1.5
> kcal/mol are okay? Any ideas on how to resolve this? I was thinking of
> constraining the aryl dihedral which causes the jumps to an intermediate
> value, but will the resulting PES be valid for dihedral optimisation?
>
> Any other suggestions are welcome.
>
> Kind regards,
>
> *Daniel Fellner BSc(Hons)*
> PhD Candidate
> School of Chemical Sciences
> University of Auckland
> Ph +64211605326
>
>