I am using HADDOCK 2.5 locally on my PC and I have to change some parameters in the .json and run.cns file to run my docking analysis. Is there a manual that explains all the parameters in these files?
I have read the manual on run.cns parameters in the Bonvin Lab website, but I can’t find an explanation of some parameters (i.e. centroid_kscale and em_kscale).
Any “kscale” parameter relates to a force constant.
For the em one it is the force constant for the EM energy term (the cross-correlation coefficient)
And the centroid one is for the centroid restraints used in the cryo-EM docking protocol.
These are not usual parameters that a user would like to change
If you dig into the run.cns file, you will find those grouped by category while the json file might list hem alphabetically