From: Kei Sit (
Date: Thu Oct 07 2010 - 21:03:31 CDT

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?