A list of online servers or programs as I know which can add hydrogens on the structures (most likely determined by X-ray crystallography).
- WHATIF server (http://swift.cmbi.ru.nl/servers/html/index.html)
–> check “Hydrogen (bonds)” in the left frame
- Molprobity server (http://molprobity.biochem.duke.edu/)
–> after uploading a PDB file, you will see “add hydrogen” in the online interface.
- HAAD: (a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures)
- PyMOL (Win/Linux/Mac)
- SPDB (Swiss PDB Viewer)
In my own test, WHATIF is more friendly for other CNS/Xplor-NIH/Haddock-related works because WHATIF generates CNS/Xplor compatible PDB format.
Molprobity generates PDB with added hydrogens but the added hydrogens are ALL numbered as “0”. Thus I have to use other program to reset all atom numbers.
PyMOL adds hydrogens,too (object -> A -> hydrogens -> add) but the nomenclature of hydrogens in proteins seems weird (see below). The hydrogens are named as H01, H02, H03.. etc. I don’t think CNS/Xplor-NIH can take it for further calculation purposes.