[Dock-fans] RMSD calculation

Thu Aug 2 02:12:47 PDT 2007

Dear all,

I usually use VMD to calculate RMSD between docking pose and
crystallized pose. But this program uses the atom numbering given in
input mol2 or pdb file to align the 2 molecules or to calculate the
RMSD. So, it doesn't work properly if the atom numbering is not the same
in the 2 files. I haven't manage yet to overcome this problem.

I welcome any suggestion.

Does anyone know if one (free) RMSD calculator exists, which uses
sub-structural search to align ligands and calculate RMSD?

Thanks for all the suggestions you could give me.

Regards,

Loraine

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