From: Sasthi Charan Mandal (
Date: Sun Mar 17 2019 - 02:07:16 CDT

Dear VMD users,
  I have calculated hydrogen bonds between protein and DNA in protein-DNA
complex using Discovery Studio and also using vmd. In vmd I can not find
atoms which participate in h-bonding, just the residues are there. And the
other thing is for single pdb vmd gives less hbonds compared to Discovery
Studio, this is one doubt and the another thing is how much percentage of
occupancy should I count for h-bond when many pdb's there. Kindly someone
help me.