Difference between revisions of "FEP+ for GPCR"

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[[File:workflow_FEP.png|thumb|center|750px]]
 
[[File:workflow_FEP.png|thumb|center|750px]]
  
 
+
* Build membrane with "system builder"
 
* Equilibration of complex structure (with confident binding pose)  
 
* Equilibration of complex structure (with confident binding pose)  
 
Carefully look into the binding site and make sure the residues are correctly protonated
 
Carefully look into the binding site and make sure the residues are correctly protonated

Revision as of 22:02, 8 March 2021

2/25/2021 Ying Yang

Steps for setting up a FEP prediction for membrane protein

Workflow FEP.png
  • 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