VMD-L Mailing List

From: Magnus Andersson (magnus_at_helium.biomol.uci.edu)
Date: Mon Aug 15 2011 - 14:26:08 CDT

Hi,

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

This helped me on one occasion.

Magnus

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