I am looking to perform RMSD analysis on my redocking results obtained using AutoDock GPU, but I am encountering a problem. I have aligned all my proteins to a reference protein and downloaded my ligand in SDF format from the PDB website. As a result, their coordinates differ. After completing the redockings, I wanted to perform an RMSD analysis, but since the location of the pdbqt file created from the sdf file is different, I am getting very high RMSD values. I thought it might be more accurate to perform RMSD analysis using the ligand file in PDB format, which I separated from my aligned protein, and the pdbqt file converted from the dlg file of my docking result. However, I then receive a warning that 'the structures are different.' In short, since my protein is in a different position from its original location, and hence the ligand file that I downloaded in sdf format and converted to pdbqt format is in a different position, I am getting very high RMSD values when I perform RMSD analysis with my docking result. Can anyone assist me in resolving this issue?