VMD-L Mailing List

From: Roshan Shrestha (roshanpra_at_gmail.com)
Date: Fri May 24 2019 - 08:55:40 CDT

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