FEP+ for GPCR: Difference between revisions

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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 18:54, 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