Your analysis will be meaningful only if you compare against the ligand-free protein. Generally if you want to analyze the stability of the protein in terms of conformational changes (which may be biologically meaningful) you probably want to look at the backbone RMSD.

A whole protein atoms calculation is going to give you a very poor RMSD, for your purpose a C-alpha is more then enough, but if your are willing, try with some other backbone atoms. Good Luck.

Thank you very much for replying.

I would also like to know the purpose of performing C-alpha RMSD calculations. What sort of information can we get about the protein?