How can i do protein and DNA-ligand docking

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Dear administrator or anyone,

I am doing the docking between protein and a DNA linked with ligand. Can HADDOCK do this kind of docking?

A covalently bound ligand will be problematic. But if you treat it as non-covalent it should work.
The ligand should have HETATM in the PDB file. And I would define a few distance restraints between your ligand and the DNA to keep it in place (upload those as unambiguous distance restraints in the distance restraints menu (requires expert access).

Thanks very much amjjbonvin. There is also a problem. The error message said the DG residule is not supported.

Use a three letter code for nucleic acid bases, i.e. GUA instead of DG

How so you convert from the two letter code to 3 letter code?

Edit the file and replace the names… make sure not to mess up column positions