Dear Francois, Actually, the UFF implementation doesn’t include partial charges. The paper says something like “you could use QEq charges” but in fact every UFF implementation I’ve seen, including from the Goddard group doesn’t include them.
My understanding is that the parameters were derived without charges to make it easier to handle periodic boundary conditions (ie no need for Ewald sums and the like). So Open Babel can compute QEq charges, but they’re not included in a UFF calculation. I actually use this as a demo in Avogadro… put a few water molecules and UFF doesn’t do much. Switch to MMFF94 and suddenly they reorient and hydrogen bond. I’ve always wanted to see a modern parameterization of UFF with polarizable electrostatics, etc. Best, Geoff On Mar 16, 2023 at 4:13 AM -0400, Francois Berenger <mli...@ligand.eu>, wrote: > Dear list, > > Am I right that rdkit has an UFF implementation, but the > recommended partial charges for UFF cannot be computed by rdkit? > Those charges are called QEq in the UFF seminal paper[1]. > > I think openbabel can compute them, but I am surprised if this is not > included in rdkit. > > Does it mean that the UFF rdkit implementation doesn't include > electrostatic > interactions? > > Will hardcore computational chemists send me to hell if I use UFF in > combination > with the MMFF94 partial charges? > > Should we include QEq charges in rdkit? (I honestly don't know yet if > this is hard > to implement) > > Thanks a lot, > Francois. > > [1] UFF, a full periodic table force field for molecular mechanics and > molecular dynamics simulations > https://pubs.acs.org/doi/abs/10.1021/ja00051a040 > > > _______________________________________________ > 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
