Is it possible to calculate ligand desolvation energies with Prime MM-GBSA?

Yes, you can do this as of Suite 2011. You will have to set the receptor charges to zero and then run MM-GBSA using the input charges. The change in solvation energy upon binding is then the ligand desolvation energy. You can set the receptor partial charges to zero in the Build panel (Edit → Build → Atom Properties, choose Partial Charge from the Property menu).

In order to use input charges, rather than force field charges, the job will have to be run from the command line:

$SCHRODINGER/prime_mmgbsa -cmae [options] pose-viewer-file

Keywords: Prime, MM-GBSA, MMGBSA

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