How can i do protein and DNA-ligand docking

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

Dear administrator or anyone,

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

2

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).

3

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

4

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

5

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

6

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