VMD-L Mailing List
From: Bret Hess (bret_hess_at_byu.edu)
Date: Mon Nov 23 2015 - 11:46:31 CST
How do I specify bonds with scripting? I'm writing a TCL script anyway.
On Mon, Nov 23, 2015 at 10:29 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Mon, Nov 23, 2015 at 11:55 AM, Bret Hess <bret_hess_at_byu.edu> 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
> > 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
-- Bret Hess Department of Physics and Astronomy Brigham Young University N251 ESC Provo, UT 84602 801-422-2108 FAX 801-422-0553