[gmx-users] Protein-Ligand MS simulation

[MUSYOKA THOMMAS]

Hello. I have a protein pdb and the best pose of a ligand obtained through
docking using auto dock. However, when I combine the ligand and protein
using the discovery studio, some residues like Lysine in the protein pdb
gets protonated as well as the N-terminal residue. Is this unusual and can
it affect the MD end results?