when i define the restraints with protein and dna/rna on local installation, the chains of nucleic acid of output structures seprates from each other, is there any restraints to be defined btween chains of nucleic acids? or is there good tutorial for this system
Make sure your restraints are properly defined with the correct segIDs and atom names that match your PDB files.
thanks for your reply, do i need to define the specific atom for nucleic acids or just define the resi is okay?
Residue is ok, but if you know that the binding is e.g. in the major groove you could use a more defined list of atoms.
We should soon have an online tutorial for protein-DNA docking