Hello, I am simulating a protein using side chain pKa values estimated from PROPKA based on crystal structure of the protein. I re-estimated the pKa of side chains after running 10 independent replica of 50ns (500ns in total) of NPT simulations. It turned out that the average pKa of a surface Glu was overestimated in the crystal structure (protonated), and needs to be reconsidered (not protonated). I was wondering how I can re-assign the protonation state of this single residue without going through pdb2gmx (or may be I have to) to keep the current conformation of the protein and currently equilibrated solvent molecules? Is there a way to continue the current simulations I have and only change the charge of this single surface Glu? Thanks for your help.
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