I want to create parameters for running constant pH md for a ligand. The
manual states that if the titrating group is a polymer subunit, then I must
adjust the charges on atoms that have bonded interactions with neighboring
residues. In my case, since I am using parameters for a free ligand, is it
safe to assume that I can use different charges for all atoms in both
protonation states?
Thank you
Fabrício
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Received on Thu Nov 10 2016 - 06:30:02 PST
