The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
Hi professor Bonvin,
The question is about the presence of hydrogen atoms. Exist some difference in haddock calculations if the hydrogen atoms are present in my input files for docking?. This question is only to refine my protein-protein docking.
King regards
Roberto Rosales
Bioinformatics engineer
We are using a united atom force field. Only the polar hydrogens are kept for protein-protein docking. You can decide to keep all hydrogens, but it will make the computations slower and should not make much difference. Of course the results won’t be the same. It all also depends on the info you have to guide the docking
Ok, so… ¿The best way to submit my pdb file for docking is with all hydrogen atoms, and Haddock will discriminate automatically or manually all the polar hydrogens?. Currently I work in haddock with pdbs that contain and not his hydrogen atoms.
Thank a lot 
Don’t bother about missing atoms. HADDOCK will automatically rebuild the missing one and discard the unnecessary ones.
Thanks a lot professor Bonvin!