From: Joao Ribeiro (
Date: Mon Jan 06 2020 - 09:20:56 CST

Hi Francesco,


Which RMSD plugin are you referring to? As you may be aware, VMD has 3 RMSD plugins.


If I understand correctly, you are trying to calculate the RMSD of the backbone of a small molecule. Are you sure that VMD understand the backbone of your small molecule? Please try to make the selection in the Graphical Representation window and check what is selected, e.g., (resname xxx) and backbone--B_3661147257_100283435--