Reduce

If you're looking for a reliable, user-friendly application that can add hydrogens to Protein DataBank (PDB) molecular structure files, you'll definitely want to give Reduce a try. This free software boasts a wide range of capabilities, including the ability to add hydrogens in standardized geometry while optimizing the orientations of OH, NH3, SH, Asn, Met methyls, and Gln sidechain amides, as well as His rings.

One of the great things about Reduce is that it can handle both proteins and nucleic acids with ease. Additionally, it can even process HET groups -- as long as the atom connectivity is provided. Luckily, a slightly modified version of the connectivity table published by the PDB is available within the program.

You should note that there are two available "flavors" of HET dictionary within Reduce -- new and old. Your choice of dictionary will depend on which type of reduced PDB you're hoping to produce as output.

Overall, Reduce is an excellent software choice for anyone looking to add hydrogens to PDB files. With its straightforward interface and high degree of flexibility, it's sure to be a valuable tool for anyone working in molecular biology or related fields.