I am trying to calculate Ddg for a protein complex, which is made of 3 chains: A, B and C.
The chains B and C have a zinc-finger each, which are a zinc ion complexed by four CYS side-chains.
To calculate the Ddg I am using the SetupPoissonBoltzmannPotential mover followed by the Ddg filter, in order to separate chain B from chain A+C and calculate the binding energy.
The problem I'm having is that to calculate Ddg, the SetupPoissonBoltzmannPotential mover creates a .pqr file for the bound form and another .pqr file for the unbound form. As you can see in the attached figure, in the unbound.pqr the chain B is separated from the others, but the zinc ion that belongs to chain B is not shifted along with chain B.
I have tried to use SetupMetalsMover to create a distance constraints in the metal binding sites, but without success.
Is there any mover specific for metalloprotein to calculate binding energy?