Hi,
I am trying to dock a protein-peptide structure. Both have HIS. I did not assign the protonated state; therefore, they should all be double protonated. However, this is the case only in the protein.
In the peptide- I start with an HD1 and when the docking starts, the begin file changes to HE2.
How can this be? why are they not both protonated?
Of course I have set delenph=false
I know, but if I don’t define it then it should be double-protonated, no?
So I don’t understand why that is not always the case
(the HIS is far from the binding zone so it is not critical what state it is in so I did not spend the time defining it- but I want to know why HADDOCK is not making it double protonated)