You can try the following:
In your pdb file, rename "LYS" to "LYN" (if you use AMBER or TYL06 forcefield in PDB2PQR) in the interested lysine residue; or, rename "LYS" to "LY0" if you use PARSE forcefield (it doesn't look like there are neutral lysine parameters in CHARMM forcefield though). Then use PDB2PQR on the modified pdb file.
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.
NathanOn Sat, Feb 21, 2009 at 12:46 AM, Kin Sing Stephen Lee <firstname.lastname@example.org> wrote:
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
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis