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.