DNA Protein Interaction


I am trying to upload DNA pdb file (which I generated from YASARA) in the “Molecule 2 - Input Section”. However, I am constantly seeing the following error
" Error in PDB file.
Issue when parsing the PDB file at line 2 .
Your PDB contains a Ligand DG but you have indicated Nucleic as molecule type. Please select “Ligand” instead."
I tried saving the DNA pdb file in pymol as well, as suggested by admin in separate discussion, but it didn’t help and showed the same error.
Please help,


Can you share your PDB file?


Thanks for your prompt response. Much Appreciated!
I couldn’t upload PDB file in my initial query as the platform didn’t allow me to “Sorry, new users can not upload attachments.”
But you can access the file using the following link:


Thanks for sharing the input file with us. The issue is that your input has HETATM records instead of ATOM for the DNA molecule.

If you simply replace HETATM for ATOM (keep in mind that in the PDB file the number of spaces is important) then you will no longer get the error and you can setup your docking run.

The error message is indeed a bit confusing, we will address that. :slight_smile:


Thank you for your help. I followed your suggestion and replaced HETATM for ATOM, but it didn’t help.
This time I notice error, which read as:
Error in PDB file.
Issue when parsing the PDB file at line 1 .
ATOM/HETATM line does not meet the expected format

You can have a look at the pdb file using the below link:

Looking forward to your response.


As I said, the whitespaces are important in a PDB file, have a look at official PDB documentation for more information.

But in summary you are missing two whitespaces after the ATOM record :slight_smile:

HETATM    1  P    DG A   1       0.390   0.321  -2.326  1.00  0.00           P

ATOM    1  P    DG A   1       0.390   0.321  -2.326  1.00  0.00           P

Hi Rodrigo,

And IT WORKED!!! Yaiyeeee!!!

Thanks a ton for your help.


Glad to hear that! Happy HADDOCKing :tada: :wink: