From: Axel Kohlmeyer (
Date: Wed Apr 15 2009 - 07:56:52 CDT

On Wed, 2009-04-15 at 13:20 +0530, Manishi Pandey wrote:
> Hi All!

hi manishi!

> 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.

kindly help _us_ to help you. VMD has no knowledge of chemistry
(and no psychic abilities either), so it relies on certain naming
conventions to detect whether an atom is a hydrogen or a hydrogen
bond donor or acceptor. for that your pdb files have to actually
contain hydrogens and have to be formatted correctly.

are you sure this is the case? can you provide a (small) example?


> Manishi

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.