Member Site › Forums › Rosetta 3 › Rosetta 3 – General › How do I add hydrogen atoms to my PDB file? › Reply To: How do I add hydrogen atoms to my PDB file?
March 30, 2011 at 3:02 pm
#5268
Anonymous
Is there a particular reason you need to pre-add hydrogens? As far as I’m aware, Rosetta will rebuild any missing atoms in input PDB files (including hydrogens) prior to using them.
If you’re looking for just the PDB with hydrogens attached, running them through the scoring application (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_score_commands.html) with the flags “-output” and “-no_optH false” should do the trick. (The latter option tells Rosetta to try to optimize polar hydrogen placement – put them in the best place for hydrogen bonding, etc.)