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
ACF.
This is a very different situation than claiming the NH2 group simply
isn't accounted for.
-Justin
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@maillist.sys.kth.se
<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,
Neena
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Justin A. Lemkul, Ph.D.
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