Hi there 
!
I’m docking a protein-protein-protein-RNA system. I found that in haddock3’s protein-DNA example cfg file, epsilon = 78;dielec = "cdie" are set for DNA case.
For RNA system, are these settings necessary? Would these settings effect Coulomb energy term between protein-protein?
Are you docking thus four molecules?
Or the RNA onto one complex of three proteins?
The settings are global, affecting thus all interfaces.
These three proteins have interfaces with the RNA respectively, and there are multiple protein-protein interfaces too.
In this case, are epsilon = 78;dielec = "cdie" suitable?
So you are docking the three proteins separately to the RNA?
You thus have a mixture of interface types. We never really benchmarked what are the best settings in this case…
It will also very much depend on the amount of information you have to drive the modelling.
E.g. if you have very good restraints between the proteins, you might want to use the nucleic acid settings to focus more on the proteins/RNA interface
That makes sense.Thank you very much!