My structure has missing residues in the middle of the sequence (discontiguous sequence). Will H++ still compute pKs and protonate the structure?
No. H++ will read in your structure and report an error. pK estimates of any kind depend critically on fine details of your structure: if chunks of the structure are missing, the computed pKs may sometimes be completely off, especially in the vicinity of the missing part. So you have to be very careful with what you do next. The safest approach is to find another PDB structure which does not have missing residues. If one is not available, there are still a couple of things you can try. If the groups you are interested in are not located in the vicinity of the structural gaps (in real 3D space, not in sequence space!), you may re-do the computation by treating discontiguous parts of the structure as separate chains. Simply insert a “TER” in each gap in the PDB and resubmit. Make sure that residues in each new “chain” are numbered sequentially, without gaps. Generally, the more residues are missing, and the closer is the group of interest to the missing space, the less reliable the resu
