VMD-L Mailing List

From: Neena Susan Eappen (neena.susaneappen_at_mail.utoronto.ca)
Date: Mon Sep 25 2023 - 14:14:33 CDT

Hello VMD users,

This is not a question related to VMD, but I was wondering if someone can help me or guide me to the appropriate resource.

I extracted two types of H-bond occupancy data (donor: Lysine side chain and backbone amide NH, with backbone carbonyl CO as acceptor) from two different trajectories of the same peptide, centroid structures from predominant cluster of each trajectory shown in each row. These structures just differ by dihedral angles across a few residues.

Question: What is the best way to quantify relative strength of total intramolecular hydrogen bonding between these two trajectories?

[image.png]
Many thanks,

Neena Eappen
Graduate Student
Jockusch Lab<https://urldefense.com/v3/__http://www.chem.utoronto.ca/wp/jockusch/__;!!DZ3fjg!7BQq4_UfJq0ad40jwPnxqL3G06aRbBD6j4Fx_-6-SB-yTf7vn4luF0F2P9KDJbOXZEMOpLXymgYArwst6Lr_uGo_2z-XOFwjY6MG$ >, U of T