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2/25/2021 Ying Yang

Steps for setting up a FEP prediction for membrane protein

Workflow FEP.png

Protein side

Carefully look into the binding site and make sure the residues are correctly protonated...

Protein model completeness Protein preparation should include fixing any chain breaks, modeling in any loop conformations and adding any missing side chains. Chain breaks near the active site will likely lead to poor results. Disulfide bridges should be created and termini residues capped where applicable.

Equilibration of complex structure (with confident binding pose)

  • Build membrane (use the OPM database), add salts, add solvent
 res.num 76-97,112-136,141,143,146-171,194-215,227-229,231-256,323-345,347,360-380,382,398
  • write job submission file
 replace gimel-biggpu to gimel5.heavygpu
  • Analyze the MD simulation

Visualize the trajectory and analyze the simulation with SID tool

SID analysis.png

  • Convert -out.cms into mae
 $SCHRODINGER/run membrane_cms2fep.py -ligand 'ligand' 2A_NBOH_MD-out.cms -o relax_2A_NBOH_pv.mae

Ligand side

Careful preparation of the ligands is critical to a successful FEP+ prediction. Best practices include running LigPrep on all the compounds to exhaustively enumerate all the stereoisomers and likely protonation states of the ligands. Note that triply-substituted ammonium cannot invert stereochemistry during the simulation, making it important to model both pseudo-stereoisomers.

  • 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