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RMSD calculation difference in Autodock and ADT

posted Jun 2, 2011, 7:30 PM by Dong Xu   [ updated Jun 2, 2011, 7:31 PM ]
This is from Ruth at Scripps:

What I am saying is that the distance between each atom in the docked conformation and the closest atom of the same element  in the reference structure is what is used for the RMSD calculation in autodock. (this is similar to Vina)

In contrast, the distance between each atom in the docked conformation and the same atom in the reference structure iswhat is used for the RMSD calculation in ADT.
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