Hi Sing --
That's an interesting question. I don't think we have parameters for neutral lysine available in any of the force fields provided with APBS but will Cc Yong and the APBS-USERS list to make sure.
I am currently trying to use APBS to calculate the electrostatic potential of my protein. In my protein, there is coupled of lysine in the binding pocket and next to each other. We have the reasons to believe that one of the lysine should not be protonated. I am wondering is there anyway I can make sure that the lysine is in neutral form after pdb2pqr? If no, is it possible for me to modify the pqr file so that it is in neutral form? what would be the potential for CB, CD, CE, NZ and NZH of the neutral lysine?
Thank you very much