VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Sat Aug 01 2020 - 16:48:19 CDT

Did you load the psf first? Otherwise vmd guesses bonding from the pdb.
Josh

On Sat, Aug 1, 2020, 11:39 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> On Jan 09 2018 11:25:28 CST John Stone wrote, inter alia, "if the PSF
> doesn't explicitly include a disulfide bond, VMD will not display it,
> end of story."
>
> I have a protein with three disulfide bonds, correctly patched when
> building psf/pdb with vmd in text mode. All three bonds can be identified
> in the psf file, although they are not displayed by VMD in bond
> representation. All that can be seen from the display is that the S-S
> distance is 2.05A in all three cases.
>
> I remember vaguely that I already had similar problems in the past,
> relying on the identification of the S-S bonds from the psf file.
>
> Is that anything I am missing when loading psf/pdb?
>
> thanks
> francesco pietra
>