HADDOCK for protein DNA docking

... you can do online.

please go through that link-

http://autodock.1369657.n2.nabble.com/protein-dna-docking-td6456871.html

Dear Somya,

You can use Hex server/software for protein-DNA docking. The range angles are to be palyed with to get good docking. I hope this helps.

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best,

Kalpana

HADDOCK for protein DNA docking

... you can do online.

Better go for QM polarization docking coz DNa and RNA containing highly electron rich atom and coz of their polarity u should do QM polarization docking.

Yes. It is possible but the size of the file in case of DNA molecule should be low or else it would take ages to complete. Select DNA (a low MB file)as the macromolecule and protein as the ligand. All the best.

Selecting protein as a ligand in pdbqt format through open babel produces some error "Unknown or inappropriate tag" while docking with RNA as a receptor using autodock vina. How to convert protein from .pdb to .pdbqt without error?