I am trying to add hydrogen atoms to dexomethasone ligand. In the original PDB file, there are two dexomethasone molecules. So, I create split them into two different PDB's. Then, I load them and use addH option. In one PDB (sil.pdb), everything works fine and all hydrogens are added successfully. However, in the other pdb (which I name as other.pdb), one hydrogen atom is missing. I will use these files for further parametrization in AMBER, so this is really important. I looked through the files over and over again but couldn't find any reason for this apparent difference. What am I missing? I also attach the files. Any help would be greatly appreciated.