Dear Users,

I want to calculate the RMSD of two ligand molecules of different atom counts but have a common scaffold.

I tried rmsd #0 #1

but I'm getting the error: unusual numbers of atoms chosen for evaluation.

rmsd #0:15-17 #1:15-17

atleast one atom must be selected.

could somebody help me to find the RMSD between two ligands of different atom counts.

regards,
Pavithra.K.B.