ADL: RMSD for a different molecule

Abdul Hameed, MohamedDiwanMo mabdu3 at
Mon Oct 1 10:21:03 PDT 2007


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.


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