In a flexible receptor docking in AutoDock 4, which atoms are used in the clustering?Up to table of contents
This FAQ applies to: AutoDock 4
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.