(Single) Amino acid rotational degrees of freedom When defining the rotational degrees of freedom for a single molecule, should we just include the psi and phi angles (red lines in the picture) or the rotation around every single bond (yellow lines in the picture) or both?
You should be concerned with bonds where the rotation is non-trivial. For example, rotation about a C-H or O-H bond doesn't do anything. But rotation around the serine side-chain C-O bound or the side-chain central carbon bond or the C-O carboxylate bond all matter.