Reading the documentation of the ddg_monomer application I noticed that minimize_with_cst is needed to reduce collisions that result in a high free-energy score. For some structures I already used the relax application to achieve this. Hence my questions:
1. What does minimize_with_cst do? And how does it differ from what the relax application does?
2. Can I use my relaxed structure as input to a low res ddg_monomer run?
Looking forward to hear from you.