Help on job https://mobyle.rpbs.univ-paris-diderot.fr/data/jobs/PEP-FOLD/Y23471734486103

justrand · May 19, 2021, 2:43pm

Hello!

I’ve been attempting to model a 21 amino acid peptide containing cysteines with the presence of a disulfide (RKCVISVARRNRRANIKILCN). I’m using Pepfold2.0 and the advanced options to input a disulfide bond (i.e. 3-21), but the model which come back do not contain any disulfide bridge. Am I doing something incorrectly? Thanks!

Session information:

id: V10021098331928
email: None
activated?: True
authenticated?: False

Job information:

id: https://mobyle.rpbs.univ-paris-diderot.fr/data/jobs/PEP-FOLD/Y23471734486103
date: Wed, 19 May 2021 16:41:01 +0000
status: submitted
user error in parameter: None
user error message: None

devries · May 26, 2021, 10:48am

Hello,
The cysteines are in close spatial proximity. From what I can see, the CB are correctly oriented as well. It looks like either Oscar-star or Gromacs refused to acknowledge the disulfide bonds. You could try to run Oscar-star or SCWRL on your own computer on the generated models, perhaps that will work.

cheers

Sjoerd

devries · June 9, 2021, 4:00pm

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