ADL: nativeness RMSD

Yong Liang Yang yonyang at
Thu Sep 30 08:10:12 PDT 2004

Dear AutoDock users:

     I have a question about how to set up and calculate
nativeness RMSD. What I exactly mean is, I am doing virtual
screening for a small molecules database, and I want to
compare each docking result with a native ligand from crystal
structure from which I could obtain the nativeness RMSD.
(in another word, how native the ligand is.)

     I tried to edit the DPF parameter file and use the native
ligand PDBQ file as reference structure. However, AutoDock complains
that there is a conflict in atom numbers between reference strucutre
and docking ligand. What is more, when I try to use the docking ligand
itself as the reference structure (default), it always gives me very
weird RMSD value such as 88.50 which I think is amazing big.

    I sincerely hope you can give me any suggestions or tips
on calculating nativeness RMSD and the scheme for Autodock
to calculate the RMSD between reference structure. (I could not
find it in manual) Your help will be greatly appreciated !
Have a good one.



    Stony Brook, 11790, N.Y.

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