# DNA Protein Interaction **URL:** \ **Category:** HADDOCK\ **Created:** [April 11, 2022, 6:35pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660 "2022-04-11T18:35:26Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![saurabhumrao](https://avatars.discourse-cdn.com/v4/letter/s/df705f/32.png) [@saurabhumrao](https://ask.bioexcel.eu/u/saurabhumrao)\ **Post date:** [April 11, 2022, 6:35pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/1 "2022-04-11T18:35:26Z")
Hello, 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, Thanks! ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [April 11, 2022, 7:03pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/2 "2022-04-11T19:03:41Z")
Can you share your PDB file? ---
**Author:** ![saurabhumrao](https://avatars.discourse-cdn.com/v4/letter/s/df705f/32.png) [@saurabhumrao](https://ask.bioexcel.eu/u/saurabhumrao)\ **Post date:** [April 11, 2022, 7:39pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/4 "2022-04-11T19:39:32Z")
Hi, 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: > **[AptPostYasara&Pymol.pdb](https://drive.google.com/file/d/1BaSdJ6iTvk4601NUQqnNDEP2c_wTF7V3/view?usp=sharing)** > > Google Drive file. Best, Saurabh ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [April 11, 2022, 8:01pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/5 "2022-04-11T20:01:02Z")
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. 🙂 ---
**Author:** ![saurabhumrao](https://avatars.discourse-cdn.com/v4/letter/s/df705f/32.png) [@saurabhumrao](https://ask.bioexcel.eu/u/saurabhumrao)\ **Post date:** [April 11, 2022, 8:47pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/6 "2022-04-11T20:47:17Z")
Hi, 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: > **[AptPostYasara&Pymol\_ATOMRepla.pdb](https://drive.google.com/file/d/1fHwUXL2s9_iKnFgSkhxe5Cm95m2VQFNR/view?usp=sharing)** > > Google Drive file. Looking forward to your response. Best, Saurabh ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [April 12, 2022, 1:26pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/7 "2022-04-12T13:26:06Z")
As I said, the whitespaces are important in a PDB file, have a look at [official PDB documentation](https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html) for more information. But in summary you are missing two whitespaces after the `ATOM` record 🙂 ```auto 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 ``` ---
**Author:** ![saurabhumrao](https://avatars.discourse-cdn.com/v4/letter/s/df705f/32.png) [@saurabhumrao](https://ask.bioexcel.eu/u/saurabhumrao)\ **Post date:** [April 12, 2022, 11:20pm UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/8 "2022-04-12T23:20:45Z")
Hi Rodrigo, And IT WORKED!!! Yaiyeeee!!! Thanks a ton for your help. Best, Saurabh ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [April 13, 2022, 8:18am UTC](https://ask.bioexcel.eu/t/dna-protein-interaction/3660/9 "2022-04-13T08:18:49Z")
Glad to hear that! Happy HADDOCKing 🎉 😉