Refinement of the models from haddock2.2 webserver


#1

Dear all,

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?

Thanks.

Best
Changdong


#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.


#3

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:

http://www.bonvinlab.org/software/haddock2.2/tips/advanced_refinement/

You need for that to use (and have access) to the guru interface


#4

Dear Dr.Alexandre Bonvin and Joao Rodrigues,

That works, thanks.

Best