Does ScoreL calculate atomic charges?
ScoreL ignores both formal and partial charges. In the case of protonation mode in docking task is set up in “from structure” ScoreL deduces whether an atom is charged by counting the bond order of the atom and comparing the result with the atom’s normal valency. In the case of protonation mode in docking task is set up in “auto” ScoreL calculates ionized states itself. For this reason, it is essential that the bond and atom types are set up correctly for both the protein and the ligand. For further information, please refer to the ScoreL documentation.
