I have recently run into some troubles trying to parametrize a ligand with the latest version of antechamber. As Sergi reported recently, the iop(6/33=2) was deleted in the revision b1 of Gaussian and replaced by the new iop(6/50=1) in the later revision c1 (available at CESCA). The fact is that in the AMBER12 guide is not clearly explained how to obtain an AMBER prep file from the new Gaussian output and for me it has being a little jigsaw. I hope this save you some headaches:
For those who need to parametrize new ligands, there is a new alternative VMD pluggin, named Paratool, to do so. It works for both AMBER and CHARMM, but has been specially designed for the latter one.
Thanks to Jordi, we could find a solution to this gaussian bug: (I wanted to parametrize a compound with iop(6/33=2) which has been deleted in our marc g09 version)
Gaussian 09 fix