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 <mli...@ligand.eu>, 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. > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
