ADL: Accurate RMSD ?

hamed ali hamed_ali37 at
Thu Jan 26 20:57:04 PST 2006

Dear all 
How can I get accurate RMSD by AutoDock,if my docked
compound has different atom no. than that of the
reference ligand, As I usually get very high RMSD with
the following error meassage in  dlg file :

ERROR!  Wrong number of atoms in reference structure.
Input PDBQ structure has 21 atoms, but reference
structure has 25 atoms.

Hamed Ismail ali
Faculty of Pharmaceutical sciences
Kobe Gakuin University-Japan

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