---
molecules:
  Abl:
    filepath: setup/2HYY-pdbfixer.pdb
    parameters: leaprc.ff14SB
  STI:
    filepath: setup/STI02.mol2
    parameters: antechamber
                
solvents:
  PME:
    nonbonded_method: CutoffPeriodic
    nonbonded_cutoff: 1*nanometer
    clearance: 10*angstroms

experiments:
  components:
    receptor: Abl
    ligand: STI
    solvent: PME
  protocol: absolute-binding

protocols:
  absolute-binding:
    phases:
      complex:
        alchemical_path:
          lambda_electrostatics: [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0, 0.0, 0,0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
          lambda_sterics:        [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0]
      solvent:
        alchemical_path:
          lambda_electrostatics: [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0, 0.0, 0,0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
          lambda_sterics:        [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0]
                
options:
  minimize: yes
  verbose: yes
  mpi: yes
  output_dir: .
  number_of_iterations: 1000
  restraint_type: harmonic
  temperature: 300*kelvin
  pressure: 1*atmosphere
  softcore_beta: 0.0

Add YAML input file for Abl:imatinib example
Add YAML input file for Abl:imatinib example
