Refinement interface query

HADDOCK
1

Hi,
Just a beginner’s query. If the restraints violation energy of my complex is high and has poor water coverage, will using the refinement interface on haddock improve upon it in this regard?

Thanks

2

The refinement interface does not use any restraints. So the restraint energy will be 0

And what do you mean by poor water coverage?

3

Thanks a lot for your reply. Sorry for the poor phrasing, I meant the percentage representation of the models generated in the third (water) iteration on HADDOCK.

4

Percentage of clustering? Number of models?

Refinement if starting from one model, will generate only one cluster

5

Got it, thanks a lot.