Simulation of whole yeast ribosome to study single residue substitution in core RP

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GROMACS version: 2023
GROMACS modification: Yes/No
I have been trying to work with yeast ribosome structure for energy minimization and md simulation. My main objective is to see effect of single aa substituion in core L8 protein on local as well allosteric changes, intersubunit communications and dynamics .I need advice regarding following points:

  1. what is suitable kind of energy minimization i can do considering massive ribosome structure?
  2. How to work with mmcif format files in Grommacs ?
  3. should i use corase grained or i can do all atom simulation in this case?