I have been docking heme B to a heme binding protein. The docking itself seems to work ok but I noticed that in the output PDB-files, “FE” is shifted to the right in the ATOM TYPE column and the right-most column says F rather than FE. As a consequence, programs such as Ligplot does not recognize the FE-atom in the centre of the heme. The input PDB-file for heme is in the correct format and the FE-atom is recognized.
I can of course easily edit the PDB-file so that the FE-atom is recognized but if the output PDB-file is wrong, perhaps the docking solutions are as well? Please advice.