From: Axel Kohlmeyer (
Date: Mon Mar 05 2007 - 08:27:12 CST

On Mon, 5 Mar 2007, Grazia Daminelli wrote:

dear grazia,

GD> I am having a problem reading charmm coordinate files with VMD 1.8.5. In
GD> the line representation of my solvated protein I see many H-H bonds
GD> where they should not exist (see water as a triangle or H-H bonds in
GD> amino groups, methyl groups ...). I worked in the past with 1.8.3 and I
GD> never had that problem.

GD> To avoid unwanted bonds I can change the representation to Dynamic BONDS
GD> or load the psf file together with the coordinates file. Still, why this
GD> new problem?

it is actually the _recommended_ way of loading trajectories, to
first read a .psf (or equivalent) to provide bonding and atom
type information and _then_ load coordinates/trajectories.

the change you're seeing may be due to some changed heuristics
or default values of what the file reader plugins extract from
the coordinate files.


GD> thanks in advance for suggestions/comments
GD> Grazia

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.