Hello,<br>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.<br>
<br>Cheers,<br>Jackson Chief Elk<br>Graduate Student<br>The University of Montana<br>Biophysics and Biochemistry<br>