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2/25/2021 Ying Yang

Steps for setting up a FEP prediction for membrane protein

Workflow FEP.png

  • Equilibration of complex structure (with confident binding pose)

Carefully look into the binding site and make sure the residues are correctly protonated Prepare the system: build the POPC membrane, add salts, add solvent

  • Force field builder

Run force field builder for all ligands

  • Flexible ligand alignment OR core constrain docking

Depends on how similar/different are the ligands to the reference/center ligand

  • Create FEP maps

  • Write out the submission file; change host; submit on gimel5 via slurm