How to calculate RMSD and binding energy from the already docked ligand-receptor
I have the following PDB file that looks like this. It is downloadable here. This 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? Any existing tools (with or without command line) that can help?
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