Hello,
I am having a question regarding protein-DNA docking case. I am trying to use HADDOCK2.2 to dock the DNA with mutated nucleotides, although I am getting errors on missing parameters for modified nucleotides as expected. Is it possible to use HADDOCK for such cases in general? How can I make parametrisation?
Best regards
Hi there
Unfortunately we don’t support any modified bases in HADDOCK.
You could try creating parameters and topologies for those yourself by duplicating current topologies in the DNA topologies and editing those to account for your modifications. This also requires defining new parameters for all new bonds/angled/impropers/dihedrals defined and defining the proper partial charges on the atoms.
All together a non-trivial process…