VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Mon Aug 15 2005 - 13:54:28 CDT

Hello everyone,
I am generating a single strand of DNA with Amber's Nucgen. However, when I
visualize it with VMD I get a message saying that there is an unusual bond
between residues 1 and 2 of the DNA strand. This message doesn't prevent VMD
from drawing the molecule. I measured the bond length and it seems fine. There
is not noticeable reason why VMD is giving this message. I wouldn't care except
that, because of this message, VMD doesn't draw the molecule correctly using the
Ribbons visualization. It leaves off the last base: the one VMD complains about.
Does anyone know how to fix this?
Thanks,
Bob Johnson