GOLD ignores both formal and partial charges. It deduces whether an atom has a formal charge by counting the bond order of the atom and comparing the result with the atom's normal valency. 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 GOLD documentation.
Formal charges will be output to the saved protein.mol2 file and to the GOLD docking poses.
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