Molecular dynamics (MD) simulations are a widely used computational chemistry method to study biomolecules. The technique has been extensively applied to study enzymes (biomolecules responsible for performing and speeding up chemical reactions in living organisms). Three-dimensional structures of enzymes have been obtained and deposited in protein databanks with the PDB file format. The files are rough and cannot be used for simulations without being modified. It is necessary to set up these files to perform MD simulations, and one of the important setup processes includes assigning protonation states of protein residues with more than one possible protonation state (His, Glu, Asp, Arg, Lys, and Cys). The main philosophy of assigning proper protonation states of titrable residues is that charged groups can only be presented on the surface of proteins, and there should be no buried charges not involved in ionic pairs. However, buried charges close to metal centers or active sites can be presented in the protein. In this talk I explain these and some practical examples of assigning protonation states.
