Hi I am currently trying to generate a pqr where I have 2cysteines protonated (called CYS) and 2 cysteines unprotonated (called CYM) what happens is, when I run pdb2pqr it unprotonates the CYS. Also, the SG charge in CYS and CYM is the same. Anyone knows what could I do in order to make pdb2pqr to recognize CYM as unprotonated CYS and keep CYS protonated?
Thanks Renato *Renato Mateus Domingos* *PhD student at Departamento de Genética e Biologia Evolutiva* *Universidade de São Paulo, Brazil* *Phone: (+55)(11)30917590*
