For an experimental study, we need a cystine connected to DAN dye. We want to check the docking with Haddock. However, we could not find anything suitable.
Hence, it will be great if someone can please provide the Haddock force field file for this, or instruct me how to make the force field for the molecule. The chemical structure of the molecule has been given below.
That’s not so simple I am afraid…
You could define it as HETATM in your PDB file, and add distance restraints to keep it attached to your protein CYS
To define the restraints see for example:
https://www.bonvinlab.org/education/biomolecular-simulations-2018/HADDOCK_tutorial/#defining-the-restraints-to-guide-the-docking
But in your case the segid should be the same for your DAN dye and the protein
