VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Sep 26 2023 - 05:32:52 CDT

Dear Neena,
There is nothing like a single "best way", only a multitude of
trade-offs depending on your needs and constraints.
For example, if the accuracy is paramount, the "best" way would be to
calculate the interaction energies on adequate quantum level but it
would be extremely costly.
The quickest evaluation could be to just measure the H...Y distance in a
X-H...Y H-bond and this alone would correlate with the H-bond strength.
In VMD, you may also get the force field approximation of the H-bond
interaction energy over a trajectory by using the "NAMD Energy" plugin
and using the donor and the acceptor groups as two interacting
selections; this is what I would advice to try.
Cheers,
Pawel

W dniu 25.09.2023 o 21:14, Neena Susan Eappen pisze:
> 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?
>
> 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