VMD-L Mailing List

From: Bret Hess (bret_hess_at_byu.edu)
Date: Mon Nov 23 2015 - 11:59:22 CST

Thanks!

On Mon, Nov 23, 2015 at 10:52 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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
>>
>
> 

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