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.



Many thanks,

From: Neena Susan Eappen
Sent: Tuesday, April 28, 2020 1:50 AM
To: gromacs.org_gmx-users@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,


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

jalem...@vt.edu | (540) 231-3129


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