I would like to define a potential between the CB atoms of a certain pair of residues in both centroid and full-atom refinement steps during Abinitio protocol. While in full-atom representation there is no ambiguity, I was wondering if the position of the CB is represented correctly in the centroid mode or this position would be the center of mass of the "super-atom" that represent the side chain, for example. If is not the first case scenario, would it be possible to calculate was it the difference between the "actual" position of CB-like atom in the centroid mode and the position it will be present in the full-atom representation? (I imagine it is a constant...).
ps. I know it would be an alternative to define in terms of CA atoms, but defining in terms of CB atoms implies an aditional accuracy to the potential.