AddHydrogensToProtein

How can I add missing hydrogens to a protein?

BALL offers a fragment database BALL::FragmentDatabase to add missing information like hydrogens and bonds to a protein and to normalize the atom names.

Do not forget to set the environment variable BALL_DATA_PATH pointing to your BALL/data directory.

#include <BALL/STRUCTURE/fragmentDB.h>

using namespace BALL;
...
 
PDBFile f("myProtein.pdb");
System S;
f >> S; 
 
// create the default-FragmentDatabase 
BALL::FragmentDB frag_db("");

// normalize the names
S.apply(frag_db.normalize_names);

// build the missing bonds
S.apply(frag_db.build_bonds);

// add missing hydrogens
S.apply(frag_db.add_hydrogens);

Note: The positions of the added hydrogens still have to be optimized. Please have a look at Energetically minimize a Protein's conformation