Thank you for spending time reading this post. We have used HADDOCK to do amyloid-peptide docking for some time. It worked very well in the past.
However, we recently encountered a case that sometimes the amyloid structure was completely blown up after docking. Like this:
The amyloid structure is completely the same in both pictures, but the peptide adopts different conformations. Is there something wrong with our amyloid structure that causes this strange result? Is there any special operation done in HADDOCK that we should be aware of?