From: George Madalin Giambasu (
Date: Mon Mar 05 2007 - 08:57:11 CST

Charmm includes an H-H bond for each water in the psf file. This for the
"shake" algorithm.
Check out the topology for TIP3P water, and you will see that bond is
generated. As soon as vmd sees the record of that bond in the psf file, it
will show it as a bond, even if it was 10 Ang. long.

so, it's normal..


On 3/5/07, Grazia Daminelli <> wrote:
> I am having a problem reading charmm coordinate files with VMD 1.8.5. In
> the line representation of my solvated protein I see many H-H bonds
> where they should not exist (see water as a triangle or H-H bonds in
> amino groups, methyl groups ...). I worked in the past with 1.8.3 and I
> never had that problem.
> To avoid unwanted bonds I can change the representation to Dynamic BONDS
> or load the psf file together with the coordinates file. Still, why this
> new problem?
> thanks in advance for suggestions/comments
> Grazia