From: Axel Kohlmeyer (
Date: Mon Mar 05 2007 - 11:56:34 CST

On Mon, 5 Mar 2007, George Madalin Giambasu wrote:

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

btw: in case you want to get rid of those bonds for display
you can source the attached script and run fixamberwater.
i've been writing this initiall for amber, but it seems to
work well with charmm topologies.


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

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.