Hi all,
I am using custom protocol called ‘Heat a Small Molecule, Minimize Each Conformation, and Cluster by RMSD ‘with Discovery Studio 2.0: (https://community.accelrys.com/message/5438)
After heating and minimizing, this protocol eventually allows me to superimpose the entire molecule based on all atoms or heavy atoms.  However, I need to know how to  superimpose conformations only over selected atoms, not the whole molecule.