Difference between revisions of "FEP+ for GPCR"

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* 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
 +
Prepare the system: build the POPC membrane, add salts, add solvent
  
  
* Force field builder
+
* Force field builder
 +
Run force field builder for all ligands
  
  
* Flexible ligand alignment OR core constrain docking
+
* Flexible ligand alignment OR core constrain docking
 +
Depends on how similar/different are the ligands to the reference/center ligand
  
  
* Create FEP maps
+
* Create FEP maps
  
  
* write out the submission file; change host; submit on gimel5 via slurm
+
* Write out the submission file; change host; submit on gimel5 via slurm

Revision as of 11:54, 26 February 2021

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