Can I limit the set of titratable groups to be included in the calculation?
Yes. But doing it blindly may be risky, as some important interactions may get left out. The advantage is, of course, speed. And, if you focus on a particular small group of residues you can take dvantage of choosing a more appropriate values of the input parameters, such as the internal dielectric. Proceed with caution. In any case, we recommend that if your structure is small enough you first do a “full” run to identify which sites do not interact strongly with the sites you want to focus on — H++ outputs a specific file that lists residues that contribute most to each pK shift. As a result of such a run you will have a “your_molecule.replaced.pqr” file (in “View all files generated for this run: Listing”) which will become your next-step input structure in PQR format. It has all ionizable groups in ther standard protonation states. Now suppose you DO NOT want residue “GLU 35” to be treated by H++ as titratable. Change its name into “GLX 35”, and it will be considered by H++ as non-
