Hello, I want to calculate the pKa shift of a buried aspartic acid residue in my protein using alchemical free energy perturbation. I do not know how to represent the individual aspartic acid attached to the protein in the required "couple-moltype" entry of the *mdp file. Any suggestions would be much appreciated.
Cheers, Jackson Chief Elk Graduate Student The University of Montana Biophysics and Biochemistry
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