I used Haddock Refinement Interface 2.4 to introduce different puntual mutations in a complex structures. The structures used as input to introduce mutations was a NMR structure of a protein complex with four Histidines not charged and with proton located on ND1 atom for all histidines. The problem was in the output, since 3 out 4 histidines moved the protons to the NE2 atom.
Now I am trying to overcome the issue by using the guru interface and by manually selecting the protonation state and type of histidine (HISD or HISE).
So my question, If I would to reproduce all parameters of Haddock Refinement interface 2.4 but setting manually the protonation state of histidines, How I can do ?
In the first attempt I used the following parameters found in a previous discussion on bioexcel:
In “Distance Restraints” :
“Define center of mass restraints to enforce contact between the molecules ” > True
“Define surface contact restraints to enforce contact between the molecules ” > True
In “Sampling parameters” :
“Number of structures for rigid body docking (it0) ” > Same as it1 and water, in your case, if you want 10 models per complex I’d suggest to use 200
“Sample 180 degrees rotated solutions during rigid body EM ” > False
In “Advanced Sampling Parameters” :
“Perform cross-docking ” > False
“Multiply the number of calculated structures by all combinations ” > True
“Randomize starting orientations ” > False
“Perform initial rigid body minimisation ” > False
“Allow translation in rigid body minimisation ” > False
“number of MD steps … ”*4 > 0 for the 4 values (respectively 500/500/1000/1000 by default)
The second questions is concerning “Multiply the number of calculated structures by all combinations:
Since the input structures are complexes, it means it leads to combine the chain A of the model 1 of the ensemble with chain B of all models?
Thank you in advance,