Difference between revisions of "FEP+ for GPCR"
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| Line 5: | Line 5: | ||
| − | + | * 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 | |
Revision as of 18:54, 26 February 2021
2/25/2021 Ying Yang
Steps for setting up a FEP prediction for membrane protein
- 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