HAAD Guide ******************** **************************************************** Hydrogens Atom ADdition (HAAD) algorithm HAAD is a software for adding hydrogen atoms in protein structures. COMPILING HAAD: ============== gfortran -ffree-form -ffree-line-length-0 -static -o HAAD haad.f90 RUNNING HAAD: ============= Hydrogen atoms in a PDB file(xx.pdb) can be added by running "./HAAD xx.pdb", the output is "xx.pdb.h". In "xx.pdb.h", the label in column 57 presents the label for the atoms that have been added by HAAD. When the value of the label is less than 2, the position of the added atom is trustable. CONTACT: ======== For question and comments, please contact: Yunqi Li (yunqi@ku.edu) or Ambrish Roy (ambyroy@umich.edu) or Yang Zhang (zhng@umich.edu). REFERENCE: ========== Please cite following paper when you use the HAAD program: Yunqi Li, Ambrish Roy and Yang Zhang. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures,2009 (to be submitted).