I am a new comer to modeller. I am trying to model a ~15AA long missing loop region in a homo-dimer. Both monomer units in the homo-dimer missing the loop region. Unfortunately, my template is a monomer unit. How can I model the loop region in both monomer together.?
I have tried modelling each monomer units separately, since the available template was a monomer. But, when I built the dimer from the modelled monomers (just by putting the modelled monomers together in a pdb file) the loop in one of the monomer got interlocked within a helix of the second monomer. Is there a different way to model the loop here?
Many thanks in advance