Optimize Polar Hydrogens

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Optimizing Ligand Polar Hydrogen placement with DOCK

If you used a program to protonate your ligand then you might need to optimize their positions.

To optimize the hydrogens on OH and SH groups, we used the following sample flex.defn:

______________________________________________________________________
name            hydroxyl
drive_id        8
minimize        1

definition      O.3 ( H )
definition      *
______________________________________________________________________
name            thiol
drive_id        8
minimize        1

definition      S.3 ( H )
definition      *
______________________________________________________________________

We ran dock with the following parameter:

orient_ligand            no
flexible_ligand          yes
minimize_ligand          yes

This is especially important if you are comparing starting energies with docked energies.