Protein atom naming in pdb files incorrect
The naming of protein atom names in pdb file by gromacs is incorrect. We are using e.g. HG12 and HE12 which means that the characters re shifted to the left in the pdb file columns. In many application this has the consequence that these atoms are interpreted as Mercury and Helium. Instead we should name the atoms 2HG1 and 2HE1 respectively, as many other applications do.