Lindsay,
For most design applications, you should be using the default “score12” score function. The hpatch score was developed to address a tendency of Rosetta to cluster hydrophobic residues on the surfaces of designs, creating hydrophobic “patches”. We believe these patches can lead to unintended oligomerization, or even aggregation, of designs. If you are designing protein surfaces and notice large amounts of hydrophobic surface area in your designs, you should consider using the score function that includes the hpatch score. The instructions for how to do this are on the documentation page for the hpatch score. You can read more about the hpatch score and why it was developed in the paper “Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches”, in Proteins 2011.
-R
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