I have several docked conformations of one ligand docked to a receptor and I would like to calculate the RMSD between each docked ligand and the native ligand after superposing the docked receptor on the native receptor. Currently my code does all the steps above but when calculating the RMSD between docked and native ligand I face a problem. Since the numbering system of the atoms of the docked ligand (after performing dock) and the native are different I can't use the atom numbering to check the correspondence. Also, using atom names we miss the symmetry in the RMSD calculation (for example in a ring).
Do you know what is the best tool (I need one which has command line option) to just compare the structures of ligands when calculating RMSD regardless of the numbering?