Hello!
I am using the haddock 2.2 guru interface to dock a protein and four-way junction. The four-way junction has four different strands, but after the docking, it is giving me the four-way junction with all the strands connected which is creating problem when I am simulating it. Can somebody help me with it?
Thanks
Add TER statements between the strands in your input PDB.
And note that what you describe as covalent bond between strands might be a visualization artifact
I have tried adding TER statements between the strands. It is showing " Atom P in residue DC 11 was not found in the rtp entry DC5 with 28 atoms while sorting atoms" when I am trying to simulate it in Gromacs.
More of a Gromacs problem I would say 
BUT if you were to use the 2.4 web server, it does offer the possibility to keep the terminal phosphate when the molecule type is nucleic acids.
Keep terminal phosphates for nucleic acids
A good reason to switch!
PS: you might require expert level to see that option