How to calculate RMSD and binding energy from the already docked ligand-receptor

[Edward Wijaya]

I have the following PDB file that looks like this.
It is downloadable here. This single PDB already contains ligand and receptor together.

The red molecule is the ligand and the yellow is the receptor.
They're already docked with ClusPro.
My question is how to calculate the RMSD and binding energy from it using Bio3D?

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[Xinqiu Yao]

Bio3D does not calculate binding free energy.

For RMSD, you need two structures of the same (or similar) molecule. In your case, the ligand and receptor are different. So, there is no meaningful definition of RMSD between them.

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