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Article ID: 541 - Last Modified:

I am trying to dock a ligand with free radicals to a receptor using Glide but I don't know how to define the atom type of the free radicals. How do I do this?

The force field used by Glide does not support free radicals, and in fact there are very few force fields for free radicals. QM methods are better suited to investigating such interactions.

Our QM/MM program QSite can treat the region of interest (including the free radical) with QM, but the bulk of the receptor with MM. However, QSite is not a docking program, so you'd have to preposition the ligand (say, by docking a non-radical form of the ligand with Glide) prior to using QSite for minimization or a transition state search.

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