Successfully submitted job returns "failed"

I successfully submitted a job to DISVIS with two molecules (one that is 486 a.a.) and the other about the same size with a cross-linking restraint file. I had to edit the .pdb files to get them past the error checks, but the job submitted fine. But the result says simply “failed”. I don’t know what to do with this as there is no guidance as to what went wrong. Any suggestions? I really need this analysis to verify which cross-links make sense and which don’t. Thanks for any help.

Which error checks did you get and what was the run identification?

*However there was indeed an issue in the server that should have been resolved now, please try again! :slight_smile:

Hello Dr. Honorato,

I am currently facing the same problem, with 2 monomers .pdb file from AlphaFold simulation and relative crosslinking restraint file. I have encountered the same problem here as status reported as failed after 5-minutes successful submission. There is no feedback of the error or identification at all. I am wondering what is going wrong here.

By the way, in another group, I applied PTM on these predicted structures via PyMOL plugin (PyTMs). It would generate a new .pse file. I am very curious if this feature is compatible by our platform, both in DisVis and HADDOCK. I would be very appreciated for your help!

Thank you!
Peter

Hi Peter

HADDOCK does support PTMs - for this you need to check the list of supported modified amino acids at:

https://bianca.science.uu.nl/haddock2.4/library

Simply changing the name of the residue in the PDB file is enough. HADDOCK will add the missing atoms.

Hey Alex,

Unfortunately, citrullination is not included in the list. Will there be any future updates that includes some extra types of PTMs?

Also, in the control group, the operation still failed without providing diagnosis what’s going wrong. I have tried the tutorial and it never gives this result. What should I do the next?

Best,
Zexin

Not so simple. We usually add those when needed (if it is not too complicated to generate the parameters).

But for the DISVIS analysis you should be able to do without it I would say

Well, thanks for your suggestions!

Hello Dr. Bonvin,

It’s Peter again. I am sorry to tell you that DISVIS status keep turning failed after minutes of job submission. Surprisingly, today I used pdb. models you provided in the tutorial but exchange the order (PRE5 to scanning chain and PUP2 to fixed chain) and modify a and b in restraints file correspondingly, and it fails quickly as well. I am really curious what’s going wrong here.

Best Wishes,
Peter

Does the standard example (i.e. noot swapped and original restraints) work?

If yes then something must be going wrong in your editing.