Hi Guys

Please, I need assistance. I have uploaded my protein into the discovery studio client, performed prepared protein, and minimized the protein using the SMART minimization algorithm. I also prepared the already docked ligand with prepare ligand function and minimized as well using the SMART minimization algorithm. However, after running CDOCKER and calculating the RMSD of the poses, the RMSD is always above 5, but if I only prepare the protein and don't minimize it but prepare the ligand and minimize the ligand, I wonderfully get RMSD around 0.2 A for all the poses and the binding conformation and binding amino acid residues is similar to what has been reported for the docked ligand. But I am confused; why so? Can I decide not to minimize my protein? What might be causing this discrepancy? Although, I have verified my protein structural quality using other online structural assessment software, and the result shows it is very quality. Does the minimization disrupt the protein quality? Please, what can I do. ANY ADVICE AND EXPERIENCE SHARING ON THIS IS MUCH APPRECIATED