VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Aug 27 2021 - 07:35:26 CDT

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!oPGQk_SDtp5dSs-VkZIx6HUuSDhovyPtwvQ6hdW7qSwql4ZM97BrG20cSbtggq3v1A$ | https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002532__;!!DZ3fjg!oPGQk_SDtp5dSs-VkZIx6HUuSDhovyPtwvQ6hdW7qSwql4ZM97BrG20cSbtggq3v1A$ ]
details here:
[ https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002532.s008__;!!DZ3fjg!oPGQk_SDtp5dSs-VkZIx6HUuSDhovyPtwvQ6hdW7qSwql4ZM97BrG20cSbuSeOZgFQ$ | https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002532.s008__;!!DZ3fjg!oPGQk_SDtp5dSs-VkZIx6HUuSDhovyPtwvQ6hdW7qSwql4ZM97BrG20cSbuSeOZgFQ$ ]

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