I feel I should know this one. I have a program looping through structures and bringing each small molecule into a single multi-state object so I can tab through the states.
create all_lig, this_ligand, 1, 1
then go on to the next one:
create all_lig, next_ligand, 1, 2
and so on....
however, the bonds get all messed up, presumably with atom names confused? I tried issuing a "rebuild all_lig" in between adding but that didn't seem to help. What am I missing?