Is there a way to see the per-atom contribution to the docking score?

If you run XP docking and write out the XP descriptors, you will be able to use the XP Visualizer to view the atoms/residues involved in some of the more complex GlideScore terms, e.g. hydrophobic enclosure. Note that you need a special license to write out XP descriptors.

If your job was originally run with SP, you can rescore your SP poses with XP, getting these terms.

There is also a script on our web site (Resources & Downloads → Script Center, in the Docking section) that computes per-atom scores from the XP descriptor data.

Keywords: per-atom scores, SP poses, XP docking, atom contribution, Glide

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