Hi everybody, I want to do a minimization of the phosphate I added to my protein. I know that it is protonated once. But I don't know at which position. How can I handle this with gromacs? Can I somehow "tell" gromacs that this phosphate is protonated once? Or shell I just protonate it at on position and run the minimization, protonate it at another position and run the minimization again?
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