VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Aug 02 2020 - 01:16:00 CDT

Yes, psf first

On Sat, Aug 1, 2020, 23:48 Josh Vermaas <joshua.vermaas_at_gmail.com> wrote:

> 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
>>
>