VMD-L Mailing List

From: Vikas Varshney (vv0210_at_gmail.com)
Date: Wed Aug 11 2010 - 12:54:07 CDT

Candy,
Use MDF and CAR format in MS and then load in VMD.
First MDF, then CAR on the top of MDF.

On Wed, Aug 11, 2010 at 5:26 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
>