The error message suggests that there is something wrong with your pdb
file. Where did they come from?
On 1 Dec 2017 6:05 pm, "Sundar" <jubilantsun...@gmail.com> wrote:
> 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
>
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