Hi all, Please I want to use a protein without any bound ligand for docking. I went through the process of protein report/prepare protein/setting backbone constraint/ minimization using SMART minimizer @ 2000 steps and defined binding sites using specific residues, following ligand preparation and minimization SMART minimizer @ 2000 steps. After all these, I run my CDOCKER protocol and analyzed my poses. But come to think of it mostly for ligand-bound protein, we usually use the bound-ligand for RSMD calculations. But for this case, is important to calculate RSMD of the protein and use it as a measure to validate docking? If yes! how do I go about it?