When AutoDock 4 performs conformational clustering on the docking results, which atoms are used in the clustering?

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When AutoDock 4 performs conformational clustering on the docking results, which atoms are used in the clustering?

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In AutoDock 4, conformational clustering is performed after all the dockings have finished if the keyword analysis is given in the docking parameter file (DPF). By default, only the atoms in the moving ligand (defined by the move keyword in the DPF) are used in the RMSD clustering calculations. There is a DPF keyword, rmsatoms that can take the argument all, that tells AutoDock 4 to include the atoms in the flexible residues in the receptor in the RMSD calculations for the clustering.

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