iChemLabs have just released version 6.1 of ChemDoodle 3D.

ChemDoodle 3D v6.1 is a significant update to ChemDoodle 3D with a focus on the molecular modeling engine. Notable additions include parallel processing support, an implementation of the General Amber Force Field, improved Minimizer widget performance, and a new tool for easily twisting bonds to change torsion angles. This update is recommended for all users.

There is a very nice introductory video available from last year that gives a great overview.