Conformer A atoms don’t “see” conformer B atoms so as far as the program is
concerned the B conformer only has the last ring.
You should set all confA atoms not in the last ring to blank conformers.
So:
last ring - A +B conformers
rest of ligand - no conformer
Thanks,
Nick
—
Hi Nick, Pavel and Herman,
Thanks for the lightning-fast tip about not using an altconf label for the
common part of the molecule. That was the solution. So obvious when you think
about it... My colleague Esko Oksanen also pointed out offline that I need to
include the last atom before the phen