Hi
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!
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
https://wenmr.science.uu.nl/haddock2.4/run/7271409541/134415-siglec7
job_params.json (91.5 KB)
thanks for the access and your effort.
I have more examples with different restraints:
https://wenmr.science.uu.nl/haddock2.4/run/7271409541/137452-s8surfaceonly
job_params.json (111.5 KB)
https://wenmr.science.uu.nl/haddock2.4/run/7271409541/137453-s8saxs
job_params (1).json (111.5 KB)
https://wenmr.science.uu.nl/haddock2.4/run/7271409541/137455-s8random
job_params (2).json (111.5 KB)
https://wenmr.science.uu.nl/haddock2.4/run/7271409541/137456-s8centermass
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:
- A.M.J.J. Bonvin, E. Karaca, P.L. Kastritis & J.P.G.L.M. Rodrigues. Correspondence: Defining distance restraints in HADDOCK. Nature Protocols 13, 1503 (2018). Free online only access
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