ADL: question about library screening

Michael Popov popov at enzyme.siobc.ras.ru
Thu Feb 24 22:38:51 PST 2005


Dear Dr. Sameer P. Kawatkar,

SPK> My question is, does mkgpf3 program puts the center of grid at the center
SPK> of macromolecule by default?

It seems that mkgpf3 puts the center of the grid at coordinates of the
ligand's root (no matter how far the ligand is from the
macromolecule).

By the way, I found Autodock to be very sensitive to initial position
of the ligand, but (to the best of my knowledge) there is no mention
about this in articles or manuals.

-- 
Sincerely yours,

Dr. Michael Popov,
Laboratory of Chemistry of the Proteolytic Enzymes,
Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry,
16/10 Miklukho-Maklaya St.,
Moscow, 117997, Russia.
mailto:popov at enzyme.siobc.ras.ru
                          







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