Hi everyone,
My system is a dimer. During the MD simulation, I can see a strong hydrogen bond formed between two lysine residues which are at the side chains of two peptides. But, the issue is lysines are unlikely to form Hydrogen bonds between side chain-side chain. Well, they can participate in hydrogen bonding via the charged epsilon-amino group, but for that lysine has to be deprotonated in the membrane. How can we check if the lysine residues are deprotonated or not. Are there any tools available or can it be done using VMD?
Thanks