From: JC Gumbart (
Date: Thu Oct 07 2010 - 23:19:28 CDT

I could think of a few reasons you get different results, such as the
parameters (e.g., angle/dist.) being different or if the selection is
updated every frame or not. If you still can't track it down, feel free to
send me a single pdb off-list where you see this discrepancy.



From: [] On Behalf Of
Kei Sit
Sent: Thursday, October 07, 2010 9:04 PM
Subject: vmd-l:


Hello all,


My name is Jacky and I am relatively new to using VMD. I have been trying to
use VMD to find hydrogen bonds between a specific residue and the rest of
its respective molecule. I have been searching the VMD mailing list and
reading anything I could find about hydrogen bond calculations. From what I
understand, if I use the HBonds Plugin to calculate the number of hydrogen
bonds across a trajectory, the results that are returned indicate the number
of donors AND acceptors if I provide two selections (Please correct me if
I'm wrong with this).


The problem I've encountered is the following:

Looking at the first eight frames that were analysed, HBonds tells me that
there are 6, 4, 4, 4, 6, 5, 5, 5 number of hydrogen bonds between the
selected residue and the molecule respectively. However, upon visual
assessment of the same trajectory plotting hydrogen bonds through the
graphical representation menu, I counted 6, 4, 3, 3, 3, 4, 4, 4 number of
hydrogen bonds between the same selections. I had used the exact same angle
and cutoffs for both methods and am a little curious as to why I am getting
these inconsistencies. This also goes against my assumption that the number
of hydrogen bonds returned by HBonds indicate donors and acceptors.


Could someone kindly explain to me what I am doing wrong or if I've
completely missed some important step?