Gaussian 09 and Antechamber12

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:

First: Starting from a pdb (or mol2) file, just generate an input for G09c1 like follows:

antechamber -i fenol.pdb -fi pdb -o fenol_char.dat -fo gcrt -gv 1 -ge fenol.gesp

By default it uses HF as functional, and 6-31G(d) as base, so remmeber to edit fenol_char.dat if you wish to use any different setting. After runing the Gaussian calculation you will have an additional output file called fenol.gesp and here the AMBER guide gets confusing. Forget about the examples it shows, if you want to generate a prepc file just execute:

antechamber -i fenol.gesp -fi gesp -o fenol.prepc -fo prepc -c resp -eq [0,1,2] -at [gaff, amber...etc]

and you will get the prep file in cartesian.

I hope it helps