From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 23 2015 - 12:31:57 CST

Sounds like a job for TopoTools!
https://sites.google.com/site/akohlmey/software/topotools

Trying to beat Axel to it...

On 23 November 2015 at 18:46, Bret Hess <bret_hess_at_byu.edu> wrote:

> 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
>> 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
>> needed).
>> and then you get the correctly formatted output automatically when
>> saving to a .psf or other capable format.
>>
>> axel.
>>
>> > 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
>