VMD-L Mailing List

From: Grazia Daminelli (Grazia.Daminelli-Widany_at_TU-Berlin.DE)
Date: Mon Mar 05 2007 - 07:48:22 CST

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