Protein-DNA refinement problem includes 8OG and 3DR modifed bases in DNA

HADDOCK
1

Hi all,

I am trying to using refinement protocol for a protein-DNA interaction. However, DNA consists modified nucleotides which are 8OG and 3DR. They have a critical role in protein-DNA function and so i want to hold them on the structure. How can i submit it on the HADDOCK 2.4 server without any error?

2

The only option would be to defined those as HETATM and add a few distance restraints to keep them in place.

The connectivity will however be lost.

3

Thanks it worked.