From: Magnus Andersson (
Date: Mon Aug 15 2011 - 14:26:08 CDT


Be sure the atom names in your structure file matches those in the forcefield files.

This helped me on one occasion.


Magnus Andersson, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
(949) 824-6993
Fax: (949) 824-8540

On Aug 15, 2011, at 9:09 AM, Moeed wrote:

> Hello all,
> I have a problem visualizing my structure in vmd. Once I load structure and trajectory files file I see some artificial bonds connecting all atoms while there is no bond between them. Has anyone any ideas why this is happening?
> Thank you,