I am docking a protein structure at different pHs. After obtaining the PDB structure, I protonate the protein at different pHs using pdb2pqr, download the structure, then use Autodock vina to dock a ligand onto the protein and calculate the energetics. Gasteiger partial charge was calculated in Autodock after removing non-polar hydrogens. The total partial charge rounds to an integer.

I observed in most protein charge calculators (e.g. pdb2pqr, prot pi), that the atomic charge was in accordance with the expected formal charge (based on residue protonation states). Still, it was very different from the Gasteiger charge I obtained from Autodock. E.g. at two different pHs, two residues changed protonation, but the Gasteiger charge only changed