[gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis

[Neena Susan Eappen]

Thank you Sahil, I will try VMD plugin for H-bond analysis.
Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file.
https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing

Many thanks,
Neena

________________________________
From: Neena Susan Eappen
Sent: Tuesday, April 28, 2020 1:50 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis

Hello gromacs users,

My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here?

Many thanks,
Neena