Short Glycan ligand segmentation

Lately my successful dockings give me results as ligand length of 1,1,2 however my ligand has length of 4 and I need it to stay as 4 length. I tried to enter connect information manually, but it didn’t work. Restraints I use surface and mass restraints. Is there a way to ensure my ligand stay as 1 piece.
Thanks for your time.

Did you check the list of supported glycans? If you have some other ones they won’t be supported by HADDOCK

Also not all linkage possibilities might be supported. Tricky systems!

Check: HADDOCK Web Server - Settings

Ligands I used consist of FUC,GAL ,SIA and NAG, all of them are supported.

Without more info we can’t help you….

Share a problematic run

How can I share a Status: FINISHED job with out posting a link or an attachment?

Direct email then.

which email adress should I send the information
job_params.json (91.5 KB)

thanks for the access and your effort.

I have more examples with different restraints:
job_params.json (111.5 KB)
job_params (1).json (111.5 KB)
job_params (2).json (111.5 KB)
job_params (3).json (111.5 KB)

Finally found the time to dig a bit more in this problem.

We simply don’t have parameters for the SIA-2-8-SIA linkage which is why those got disconnected.

Can I do something to fix this or prevent it from happening?

The best you can do at this time would be to define a few distance restraints between the two units. But it won’t be perfect

Is there a tool or a method to define (I know pymol gives distance). And how can I add that information to my pdb files or define it on online haddock server?

You need to measure it (e.g. in Pymol) and define a distance restraint in CNS format.

See for an example:

I have generated the .tbl file, where can I upload the file on the haddock server?

You need expert access level and then can upload it in the distance tab (third step in the submission process).

Upload it as unambiguous restraints

It works thanks for your effort