[Open Babel] Obabel warning while pdb to sdf conversion

[Sundar <jub...@gm...>]

Hi Openbabel users,

I have a following warnings while trying to convert a set pdbs to sdf or
smi. Can someone give an insight on it?

obabel pdb/*.pdb -O test.sdf
==============================
*** Open Babel Warning  in parseAtomRecord
  WARNING: Problems reading a PDB file
  Problems reading a HETATM or ATOM record.
  According to the PDB specification,
  columns 77-78 should contain the element symbol of an atom.
  but OpenBabel found '  ' (atom 1)
.
.
.
.
same error 32 times with (atom 1) to (atom 32). I was converting a total of
~8000 pdbs.

I don't have columns 77-78 in my pdbs.

Thanks,
Sundr