Creating duplex DNA structure file

Hi Everyone,

I am having issues with making a DNA structure that functions properly with HADDOCK2.4.

Initially I created a B-form duplex DNA on PyMOL. However, that didn’t work, when I uploaded the structure to haddock It did not recognize it as DNA. Instead it recognized it as a ligand. I abandon that and created a B-form DNA duplex with UCSF Chimera. When uploading that structure to HADDOCK2.4 haddock it asked me to split the two chains (A and B). This didn’t make since since each chais was already separated. I abandon this as-well.

I did more re-searching and I found that 3D-DART is the program to use when creating DNA structures for HADDOCK. I attempted to visit the webpage but all the link’s I tried did not work.

Any advice would be helpful. I am open to revisiting pymol, Chimera, or if possible trying 3D-DART.



Hi Jenaro

The DNA should be provided as one molecule, i.e. single chain with no overlap in numbering of the bases.
Further the 2.4 server follows the PDB naming:

Supported nucleic acid basesDNA
  • DA: Adenine

  • DC: Cytosine

  • DG: Guanidine

  • DT: Thymidine


  • A: Adenine

  • C: Cytosine

  • G: Guanidine

  • U: Uridine


Thanks for the feed back. The overlapping numbering was causing the issue with the Chimera DNA structure.

Heres how I solved it.

  1. First I created a DNA duplex structure on UCSF Chimera by using:
    Tools --> structural editing --> Built structure.
    This will create a duplex DNA with two chains(A & B), with the same numbering.

  2. Then I had to renumber chain B. I did this going to:
    Tools --> structure editing --> renumber residue.

  3. saved structure as pdb.

  4. Use in HADDOCK
    Haddock was able to take this structure with no problem.


Glad you solved it and thanks for posting your recipe!