Don’t use -maxwarn as it will allow you to bypass potentially significant problems.
The remainder of the warnings indicate your ligand topology has parameters that already exist in the force field (likely coming from a version mismatch between the CGenFF web server and the provided CHARMM36 port that I can do nothing about, sorry).
The missing parameters warnings indicate that parameters that should be in the ligand topology are not there. Check to make sure you haven’t edited those out inappropriately.