I have two domains that are asymmetric and I want to dock them using topology broker (asymmetric fold and dock like operation). Below is the full description of my problem:
1. I have pdbs for two domains that I want to dock. Domain1 has 3 chains and domain2 and 1 chain
2. Domain1 has a 7 residue linker and domain2 has 5 residue linker that needs to be flexible. I can possibly set this using RigidChunkClaimer in the topology broker file. My first question is, Since there are two linkers in two PDBs, should I have two claimers to define the rigid region? What is the right way to define these rigid chunk claimers for both the domains?
3. Then there are constraints between these two domains. For example, distance constraint between chain1 of domain1 and chain 1 of domain2; chain2 of domain1 and chain1 of domain2. I have all the constraints in 1 cst file. My next question is, how do I create constraint that belongs to two different domains (or pdbs) in one cst file for broker to understand the csts?