I did a flexible docking using Discovery Studio for one of the ligands which we are interested in and ranked the top poses based on the cdocking score. I wish to simulate the best pose. When I saved the desired pose of the protein-ligand complex as a single file and proceeded for solvation in the simulation module, it ended up in fatal error: molecule can not be typed with the selected forcefield (detailed that a particular residue has unusual chemical bonding which is not defined in the forcefield). When I cross-checked the structure in pymol, the ligand was on heavy clash with the side chain atoms of the same residue which we din't not see in the discovery studio. When I did in situ minimization for the docked pose first and then run solvation, there was no error and it was found okay. But the resulting structure may not be as same as the docked pose. Or can I compare the unminimized and minimized structures, the RMSD for the particular residue and the ligand are negotiable and proceed with simulations?