From: Axel Kohlmeyer (
Date: Sat Aug 11 2012 - 23:28:48 CDT

On Sat, Aug 11, 2012 at 2:28 AM, Fatemesadat Emami <> wrote:
> Dear vmd users,
> I have made the pdb/psf files for a mica surface (from the insight car/mdf


> files). When I load the psf and pdbs into the vmd it does not show some of
> the Al-O bonds (which are longer than other ~1.8-1.95 Ang). This is while I
> have loaded the psf file which includes all the right connectivities.

does it? how do you know?

> Material Studio visualizes the the same pdb correctly. Does anyone know why

pdb files (usually) don't have connectivity information.

> vmd does not show these longer bonds? Shouldn't the psf file specify all the
> bonds, if not then should I load it at all !?

it is impossible to say anything without seeing the files
or knowing more about them.


> Thanks in advance
> Fatima
> --
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department
> The University of Akron

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.