From: Axel Kohlmeyer (
Date: Mon Nov 23 2015 - 11:29:58 CST

On Mon, Nov 23, 2015 at 11:55 AM, Bret Hess <> wrote:
> I'm using VMD with VASP output. I'd like to specify bonds in a PSF file, as
> I hear it's the only way to specify them in VMD.

no. it is just convenient.

VMD can guess bonds based on atomic radii and you can set bonds via
scripting. the latter can be a bit tedious with the built in script
interface, but you can use the topotools plugin commands to add or
delete bonds explicitly in a more convenient fashion.

to record the bonding topology, you can save the data in a .psf file,
or any other file format that supports storing bonds in addition to
atom data and coordinates.

> Since I'm not working with proteins, what skeletal content in the PSF file
> can I use to get VMD to read the bonds part?

i find building the topology from inside VMD the most convenient way
(usually by starting from a guess and then making corrections, if
and then you get the correctly formatted output automatically when
saving to a .psf or other capable format.


> Thanks,
> Bret
> --
> Bret Hess
> Department of Physics and Astronomy
> Brigham Young University
> N251 ESC
> Provo, UT 84602
> 801-422-2108
> FAX 801-422-0553

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.