VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Mon Aug 29 2005 - 10:56:06 CDT

Hello everyone,
Whenever I load a DNA strand into VMD 1.8.3 I get the following error:
"Unusual bond between residues 1 and 2"
There is really nothing wrong with the bond.

This bond is actually between the terminal 5' DNA base and the rest of the
chain. The 3' terminal base does not generate an error. Even though VMD
generates an error message, the DNA molecule is still drawn correctly
(including the 5' end) with all Drawing Methods except for Ribbons. When I
switch to Ribbions visualization, the 5' base is not drawn.

I remember reading on a forum that VMD has trouble with the terminal ends of
proteins and DNA strands. Is there a way to fix this problem?
Thanks,
Bob Johnson