Ligand structure changes after docking

Hi everyone,
I am using HADDOCK 2.2 and 2.4 for RNA_ligand docking. I have a problem about changes in my ligand after docking. I prepared my ligand in two different ways (MOE_Wash and geometric optimization using GAMESS). However, after the docking I found that I am getting a different protonation state of the ligand (some bonds will change from double to single and a resonance appear in the system). I also used PRODRG for making the input file of the ligand, by only keeping the polar hydrogens, however I am still getting the same results. Does anyone experienced the same problem and a possible solution?

You don’t have control on this on the server.
The only solution would be to run a local version of HADDOCK and provide the required ligand topology and parameter files in CNS format.

Software like acpype can be useful for this. E.g.: