Article ID: 782 - Last Modified: May 16, 2011
The Glide manual reports that for the RMSD only the heavy atoms are considered. Are the hydrogens considered during the calculation of the maximum atomic displacement?
The maximum atomic displacements are calculated only for heavy atoms, just like the RMSD. There is an exception to this — if you generate more than 10 poses per ligand, Glide does not consider symmetries when determining the RMSDs (due to the computational cost), and this alternative calculation method does include hydrogens when computing the displacements.
Keywords: hydrogens, Glide, maximum atomic displacement, heavy atoms
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