The question about the file needed by haddock3 cfg file

HADDOCK
1

Sorry to bother you , there is a question about how to generate the tbl,param and top file . As i checked the manual instruction and former question asked by others . Could i get tbl file by using restrain_bodies.py script and using haddock 2.4/2.5 to get param and top file for the ligand ?

2

Dear skolae,

  • the restrain_bodies.py script can indeed generate tbl files but it will contain only restraints keeping potential chain fragments / chain breaks in relative place to each other. To generate a actual ambiguous restraint file, I would suggest to use either GenTBL webserver, or the haddock-restraints tool.
  • To generate parameters and topology files for ligands, there is currently no built in solution provided in local versions of the haddock2.X series. But we perform it on the fly when you use the webserver, when you are providing a ligand falling outside of the haddock library.

Cheers

3

Dear Victor ，

Thank you for the response , it will be very helpful.

Best regards,

Huangfu Yifan

Victor Reys via BioExcel <notifications@bioexcel.discoursemail.com> 于2025年4月14日周一 15:44写道：