Why does pdb2gmx try to replace “LYS” with “LYN”?
This is due to a substring comparison in pdb2gmx that automatically renames any residues with names containing “LYS” or “CYS” with the “LYSH” and “CYS” nomers. Because of this hard coding, we cannot offer a simple work around to maintain the AMBER residue nomenclaure. As discussed on the website, renaming LYS residues to LYP (Lysine positive) in your .pdb file will get rid of these warnings and keep pdb2gmx from trying to use LYN (unprotonated Lysine neutral).
