I hope you are doing well. I am trying to model the position of a small protein complex within a larger assembly based on EM, crosslinking data, and high-resolution structures of the individual complexes in PDB format, but I am having a bit of an issue getting things to work properly.
Specifically, the small complex is made up of three proteins with one of these physically linking the two complexes together. Two regions in the linking protein are highly resolved within each complex, with a flexible linker in between. As such, I would simply like to simulate the two complexes as rigid bodies, have the linking region be flexible, and observe how the small complex may fill a low-resolution volume within the EM, as informed by XL-MS data and the linking protein region.
However, when I attempt the simulation, the fragment of the linker protein supposed to attach to the larger complex is not static relative to the larger complex. I think this may be either an issue with system representation in the topology file or perhaps something else that the community may have faced before and could help me out with.
I would appreciate any suggestions you may have.