In TNT the type of an atom is specified in a completely separate field than the atom name. In PDB format, the atom name field specifies both pieces of information. That method is not specific enough for refinement. If you had an iron atom, does it have a +2 or +3 charge? The scattering is different but the information is not in the PDB file. If an element has only one possible ionization state from_pdb will produce the proper entry in your coordinate file. If there is more than one possible state you will have to edit your coordinate file to change the atom type.
Many programs do not write PDB format files correctly. One of the most common errors is to misplace the atom name of metal atoms. If your PDB format file contains this error it is quite possible, for example, that a nickel atom will be misidentified as nitrogen. You should inspect the metal atoms of your TNT coordinate file to ensure that the proper elemental type is written in the first column after the keyword ATOMC. If this mistake is made and refinement is attempted with the errant file the B factor of the affected atom will refine to a very low value.