I need help with Ca-RMSD calculation. I've used docking protocol to generate some models and now I want to calculate Ca-RMSD between these models and the native. Each model has 5 chains: e.g. model_AB_CDE. I want to calculate Ca-RMSD in a way that the model_AB chains would be aligned on native_AB and the RMSD between model_CDE and Native CDE will be computed. How can I do that? I've used score protocol but it computes the total RMSD between all the chains.
Thanks in advance,