From: Todd Ewing <[email-masked]>

Lone pairs in the mol2 file for grid input should be no
problem, just make sure that the LP atom type exists
in your vdw.defn file and that it has a non-zero but
small radius and well-depth.  Also make a molecular
surface for the protein with no hydrogens or lone pairs
using ms with MIDAS package or QCPE, and use that
for sphgen input.

Good luck!

Todd