How to protonate a receptor for docking?

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DOCK FAQ: How do I protonate a receptor for docking?

The program Chimera, which is free for academics and can be downloaded from, can add hydrogens to receptors. There is a tutorial on our web site at that goes through how to prepare a receptor for Grid_Score. Follow these instructions and then, before saving, type "del HC" into the command line. This comand will delete all hydrogens attached to carbons, leaving just the polar hydrogens. In answer to your other question, the Hawkins GB/SA does not require grids at all, although you have to option of using the grids generated by the GRID accessory to calculate the vdw term.

credit: Terry Lang