FEP+ for GPCR: Difference between revisions
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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
- 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