VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 14 2010 - 02:36:38 CST

On Mon, Dec 13, 2010 at 4:21 PM, Nicolas Tilmans <ntilmans_at_stanford.edu> wrote:
> Hello,
>
> I'm trying to display H-bonds, and for some reason the HBONDs draw style doesn't seem to work for me. I've tried relaxing the parameters, with no results. I've also tried to walk through the tutorial linked at:
>
> http://community.middlebury.edu/~chem/chemistry/class/bio/ch324/handouts/L6_VMD-tutorial.pdf
>
> using ubiquitin as the example molecule. Everything seems fine until I get to the HBOND section. At that point, I cannot get my VMD to reproduce the image from the tutorial. The separate "Hydrogen Bonds" section in the analysis menu also apparently fails to find any H-bonds. What am I doing wrong?

have you checked that you ubiquitin file actually does
have any hydrogens? most files from the pdb don't.

axel.

> I'm running VMD 1.8.7 MacOS X OpenGL (Intel x86)  (no CUDA support)
>
> Any help would be much appreciated,
>
>
> Nicolas Tilmans
>
>
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.