I’ve created a KNIME workflow that generates conformers, runs a geometry optimisation and keeps the lowest energy conformer:
MarvinSketch => RDKit from Molecule => RDKit Add Conformer => RDKIT Optimize Geometry
However, when I run the geometry optimisation on Bodipys I run into problems with the MMFF94 and MMFF94s force fields:
Force field creation failed. Creating empty output.
UFF works but it doesn’t always give the optimal conformer. My feeling is that the charges or the non-standard bond order (quaternary borate or nitrogen cation?) don’t go along with the MMFF force fields.
I’ve tried neutral representation as well as many different sanitization steps - but no luck.
Has anyone had a similar experience and, ideally, come across a solution?
sample SMILES: F[B-]1(F)N2C(\C=C\C3=CC=CC=C3)=CC=C2C(=C2C=CC(\C=C\C3=CC=CC=C3)=[N+]12)C1=CC=CC=C1