Can I do not penalise the unused active residues?

I would like to include all the CDR residues as active for the Fab. However, I do not want them to be penalised if they do not involve in interacting. Could this be possible?

My understanding for the algorithm is:
maximise the objective function
objective function = f_used(resi i, j, k, …) - f_unused(resi x, y, z, …)

Can I change it like this:
objective function = f_used(resi i, j, k, …)

Not possible…

But you can rescore the models in that way provided you write your own scoring function

Thanks, can I ask if this thought is reasonable?

My second thought is, the feature of HADDOCK is, it uses user-defined active/passive residues to guide the interaction. If the active residues are not penalised when not used, this unique feature will disappear, and makes HADDOCK similar to e.g. AutoDock.

It is indeed :slight_smile: