Dear Gromacs Users!
I'd like to change default protonation state of some specified Glu and Asp residues im my protein. By defaylt pdb2gmx -ignh create unprotonated state of the negatively charged residues but I want to make 2 of such residues protonated to mimick some intermollecular interactions. How I could make such edition to my structure ? Is it possible to make such changing AFTER pdb2gmx processing of my structure ( manually editiong GRO or PDB file and TOPOLOGY)? Thanks James
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