Schmid, Dr R. wrote: > I am trying to model a protein with a ligand using the "/." construct in the alignment and I am getting the following error: > > [ralf@localhost models]$ mod8v2 tens1.top > forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
This is Fortran's somewhat cryptic way of saying your PDB file is corrupt. (It doesn't happen when you don't use a ligand, because the corrupt line in your PDB file is in a HETATM record.)
The PDB format is very strict, and your HETATM records are in fact invalid - they have tab characters in them rather than spaces. Perhaps you edited the PDB file in a text editor, and inadvertently replaced some of the spaces with tabs? (The original 1d5r in PDB is not corrupt in this way.)
The fix is simple - replace the tabs with the correct number of spaces, so that your HETATM lines line up correctly with the ATOM records above them.
Ben Webb, Modeller Caretaker