From: Fatemesadat Emami (
Date: Fri Aug 10 2012 - 19:28:42 CDT

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.
Material Studio visualizes the the same pdb correctly. Does anyone know why
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 !?
Thanks in advance

*Yours Sincerely,
Fateme Sadat Emami
Nano Scale Laboratory
Polymer Engineering Department
The University of Akron*