VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 23 2015 - 11:52:04 CST

You can load a system of yours (without bonds) into VMD and write out a PSF
file for it from VMD to get a template:
[atomselect top all] writepsf template.psf

>From there it's only a matter of adding the number of bonds instead of 0 in
the "NBOND" header, and in the following lines, pairs of space-separated
atom numbers (1-based) indicating bonded atoms in fields of width 8,
wrapped every 4 pairs. Here is an example for 8 bonds:

       8 !NBOND: bonds
       1 4 2 1 3 1 4 5
       6 4 6 7 6 8 6 9

Best,
Jerome

On 23 November 2015 at 17:55, 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.
>
> 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?
>
> Thanks,
>
> Bret
>
>
> --
> Bret Hess
> Department of Physics and Astronomy
> Brigham Young University
> N251 ESC
> Provo, UT 84602
> 801-422-2108
> FAX 801-422-0553
>