As the models generated from haddock2.2 webserver only contain the protons bonded to a polar atom, I want to refine these models in water plus the NOE constraints ( the input structures for docking calculated by NMR).
Is there a way only to do the water refinement by using the local installation haddock2.2?
There is an option in the ‘Expert Interface’ to keep all hydrogens in the molecule, under the ‘Distance Restraints’ tab. Ask for a higher access level and you will be able to use NOE restraints during the refinement.
And to mimic the refinement interface settings, while keeping all hydrogens as explained above by Joao follow the recipe given on the HADDOCK manual pages at:
You need for that to use (and have access) to the guru interface
Dear Dr.Alexandre Bonvin and Joao Rodrigues,
That works, thanks.