How to display Hydrogen bonds

1. using VMD
(1) load *.pdb file
(2) 'graphics' menu  -->  'representations'  -->  'create Rep'
(3) in 'Selected Atoms' section, type "name N O" or "index 0 to 100"  (0 = starting atom, 100 = ending atom), and then hit 'enter key'
(4) select "Hbonds" in 'drawing method' section
(5) adjust distance cutoff and angle cutoff (e.g., 3.6, 30)

e.g.,  http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/img10.gif



2. using Avogadro
(1) load *.xyz or *.pdb file
(2) in display panel, check 'hydrogen bond"
(3) in the hydrogen bond section, set cutoffs (e.g., 3.6, 150)