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

Justin Lemkul jalemkul at vt.edu
Tue May 5 20:03:47 CEST 2020

On 5/5/20 12:12 PM, Neena Susan Eappen wrote:
> 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.

This is what gmx hbond does by default, see gmx help hbond:

  -[no]merge                 (yes)
            H-bonds between the same donor and acceptor, but with different
            hydrogen are treated as a single H-bond. Mainly important 
for the

This is a very different situation than claiming the NH2 group simply 
isn't accounted for.


> 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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