FEP+ for GPCR

2/25/2021 Ying Yang

Steps for setting up a FEP prediction for membrane protein

• Build membrane with "system builder"
• 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