When I select 'Calculate rmsd to input sructure' in the Glide Ligand Docking panel, does this do the calculation based on all atoms or just heavy atoms, and does it superimpose the structures to find the best fit or do it 'in place'?

The "Compute RMSD to input ligand geometries" feature on the Output tab of the Ligand Docking panel does an in-place RMSD calculation with heavy atoms only.

Keywords: RMSD, calculate rmsd to input ligand, in-place, heavy atoms, Glide

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