VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 11 2010 - 04:26:56 CDT

On Wed, Aug 11, 2010 at 2:49 AM, candy deck <candy76_at_hotmail.co.uk> wrote:
> Hello,
>
> I'm working on adsorption of dioxins into zeollite.
> All the structures are built with Material studio and then exported (.pdb)
> to be visualized with VMD.

exporting to .pdb for non-biological systems is often
a bad idea. the .pdb format only stores a subset of
the system information.

> However, the structure is different. Some bonds are missing and the nature
> of some atoms is different.

please check, if your .pdb file has any CONECT records.
if not, there is no information about bonding and VMD will
try to guess the bonds, based on internal heuristics. for
non-biological systems, those heuristics are not always
giving very good results.

it would be better to use more descriptive file formal.

what do you mean by "nature of some atoms"?

axel.

> Can you help ???
>
> Thanks
>
> Candy
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.