VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Apr 15 2009 - 03:56:52 CDT

"Distance" in VMD means not the distance between the donor H & acceptor atom, but

between the heavy atom to which the donor H is attached & the acceptor atom, so you might

not have gone to large enough distances. Also,

you need to create a separate hbond representation [choose it where you select line, cartoon, etc].

in order to display them. It's my experience that there are far fewer h-bonds than you

suspect from crystal structures, unless you're working with a neutron diffraction structure

that has actually imaged the H. Being close enough to h-bond does not guarantee that the

H will be situated so as to form the proper angle with the two heavy atoms.

 

Irene Newhouse

 

Date: Wed, 15 Apr 2009 13:20:29 +0530
Subject: vmd-l: Problem in finding the HBonds
From: manishi.pandey03_at_gmail.com
To: vmd-l_at_ks.uiuc.edu

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

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