I would like to study the aggregation of a protein in the different PHs.
To this aim I run MD simulatiopn in Gromacs and set the protenition state regarding to the desired PH.
Then I used the final frame of the Gromacs output as the in put of the Haddock AND docked this pdb with itself.
But the results are not confirmed by the experiments. I think it need to add H+ in the invironment.
Is it possible that we add a spesific concenteration of the H+ to the solvetion IN haddock?
The simple answer is no…
The only control you can have is about the protonation state of Histidines.