VMD-L Mailing List

From: Manishi Pandey (manishi.pandey03_at_gmail.com)
Date: Wed Apr 15 2009 - 02:50:29 CDT

Hi All!

I am relatively new to VMD. I want to analyze the hydrogen bonds formed
between a set of residues and ligands. I referred the manual and tried to do
it accordingly i.e. I chose the residues to be analyzed and ligand; then
Create Rep; Changed the Drawing method to HBonds. I tried the following with
about 5 PDB files but I was not able to observe any hydrogen bond in any of
them. I increased the value of Distance cutoff, Angle cutoff and Line
thickness. Related papers are showing hydrogen bonds between those set of
residues. Kindly help me to get out of this problem.

Manishi