For DNA-protein docking, my group (not me personally) has successfully used the HADDOCK package, provided you have an idea of where the binding sites are on the two molecules: http://www.nmr.chem.uu.nl/haddock/

You have AUTODOCK or VINA, very good and 'free' docking softwares. The results will depend on the algorithm, so you have to test as many as you can ir order to assess the accuracy of your results.

Dear sir,

Ricardo Ferreira ,

Thank you so much sir for your time , but i have been already used vina but there are little problem to convert into pdbqt file format when he convert it....i will tell you more detail if i ll get it again or whenever i use Vina or Autodock. (its bcz right now i am busy with diff task and looking for my phd in anywhere in the world )