ADL: RMSD for a different molecule

L. Michel Espinoza-Fonseca mef at
Mon Oct 1 10:57:11 PDT 2007

Most probably the problem here is that your reference ligand (i.e.,
the one taken from the PDB) doesn't have any hydrogen atoms, whereas
your docked ligand might have, at least, one polar hydrogen. In this
case, you have to select only the heavy atoms for both molecules, then
do the fit again.


2007/10/1, Abdul Hameed, MohamedDiwanMo <mabdu3 at>:
> Hello,
> I am trying to find the RMSD between a crystal ligand and a set of related docked ligands (all have the same core). But I am getting an error message "Reference molecule must have same number of atoms as docked ligand molecule."
> It will be very helpful if someone can tell me how to do the RMSD calculations using different reference molecule having the same core scaffold.
> Thanks in advance.
> Regards,
> Diwan
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