VMD-L Mailing List

From: Matthias Negri (thias_at_scfarm.unibo.it)
Date: Mon Aug 29 2005 - 04:19:19 CDT

Hello, I have some problems while visualizing AMBER trajectories and
making movies from AMBER crd-files!
I'm working on a protein/DNA complex.
If I convert the crd-file in a pdb, the complex looks good, with
acceptable geometrical values, according to ptraj and Procheck. But if I
watch the crd file in VMD, the complex results distorted, specially one
DNA helix is changed in size,form AND position!! (and that even if it
doesn't result in the pdb. What's the reason for?
I nedd to create a good trajectory movie, but it seems harder as I
thought! Is it because of the DNA?

Any help or hint would be appreceated, thanks in advance

Matthias Negri
thias_at_scfarm.unibo.it