I want to perform task almost as in the FAQ #1
<https://salilab.org/modeller/FAQ.html#1>: I have two separate proteins,
and want to receive one -- where these two are joined by the [G4S]n
linker. The major difference from the example in FAQ that I have the
exact orientation of both domains (they are docked onto the same
receptor at different sites), and I want them to be prohibited from
movement. The common protocol moves the downstream domain so it changes
its position and orientation, but I have to basically "freeze" the both
domains, allowing the linker to fullfill the space between them.
Either merge the two domains into one PDB file and treat them as a
single template with two chains (in which case Modeller will generate
inter-chain restraints and keep the input orientation), or deselect
those two domains so that Modeller does not refine them, as per
https://salilab.org/modeller/9.23/manual/node23.html