Re: [Rdkit-discuss] How to decompose the UFF (or MMFF94) scoring of a small molecule?

[Geoffrey H. <geo...@gm...>]

But it’s not so simple. If you rotate a dihedral, all the non-bonded VdW interactions also change.

Calculating a force field energy at one particular geometry is extremely fast, and the current version allows you to run multiple energies in parallel.

Generate a bunch of geometries at once and then score those in parallel. Trying to “update” isn’t worth it, because there are always more non-bonded interactions (n^2) than bonds and angles.

-Geoff
On May 18, 2023 at 4:24 AM -0400, Francois Berenger <ml...@li...>, wrote:
> Dear list,
>
> I asked this question in rdkit's github discussions:
>
> https://github.com/rdkit/rdkit/discussions/6377
>
> But, apparently that's not more responsive than the ML, so here is my
> question:
> ---
> I have a ligand, I would like to score its current conformer using
> rdkit's UFF implementation.
>
> Later, I would like to change some rotatable bond (single bond out of
> ring) and update
> the conformer's energy bu just re-evaluating the part of the energy that
> is supposed to have
> changed (i.e. the dihedral component).
> Bond lengths, bond angles and partial charges being constant.
>
> I suspect it should be faster than rescoring the conformer from scratch.
>
> How to do this with rdkit?
> ---
>
> Thanks a lot,
> Francois.
>
>
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