<commit_before>---
options:
  minimize: yes
  verbose: yes
  output_dir: .
  number_of_iterations: 1000
  nsteps_per_iteration: 500
  temperature: 300*kelvin
  pressure: 1*atmosphere
  restraint_type: Boresch
  softcore_beta: 0.0

molecules:
  Abl:
    filepath: input/2HYY-pdbfixer.pdb
  STI:
    filepath: input/STI02.mol2
    openeye:
      quacpac: am1-bcc
    antechamber:
      charge_method: null

solvents:
  pme:
    nonbonded_method: PME
    nonbonded_cutoff: 9*angstroms
    clearance: 12*angstroms
    positive_ion: Na+
    negative_ion: Cl-

  rf:
    nonbonded_method: CutoffPeriodic
    nonbonded_cutoff: 9*angstroms
    clearance: 12*angstroms
    positive_ion: Na+
    negative_ion: Cl-

systems:
  Abl-STI:
    receptor: Abl
    ligand: STI
    solvent: pme
    leap:
      parameters: [leaprc.ff14SB, leaprc.gaff, frcmod.ionsjc_tip3p]

protocols:
  absolute-binding:
    complex:
      alchemical_path:
        lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
        lambda_sterics:        [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
    solvent:
      alchemical_path:<commit_msg>Make sure we also include the free energy of turning on restraints<commit_after>---
options:
  minimize: yes
  verbose: yes
  output_dir: .
  number_of_iterations: 1000
  nsteps_per_iteration: 500
  temperature: 300*kelvin
  pressure: 1*atmosphere
  restraint_type: Boresch
  softcore_beta: 0.0

molecules:
  Abl:
    filepath: input/2HYY-pdbfixer.pdb
  STI:
    filepath: input/STI02.mol2
    openeye:
      quacpac: am1-bcc
    antechamber:
      charge_method: null

solvents:
  pme:
    nonbonded_method: PME
    nonbonded_cutoff: 9*angstroms
    clearance: 12*angstroms
    positive_ion: Na+
    negative_ion: Cl-

  rf:
    nonbonded_method: CutoffPeriodic
    nonbonded_cutoff: 9*angstroms
    clearance: 12*angstroms
    positive_ion: Na+
    negative_ion: Cl-

systems:
  Abl-STI:
    receptor: Abl
    ligand: STI
    solvent: pme
    leap:
      parameters: [leaprc.ff14SB, leaprc.gaff, frcmod.ionsjc_tip3p]

protocols:
  absolute-binding:
    complex:
      alchemical_path:
        lambda_restraints:     [0.00, 0.25, 0.50, 0.75, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
        lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
        lambda_sterics:        [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
    solvent:
      alchemical_path:
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{'dir': 'git-commits-cleaned', 'id': '3092675', 'n_tokens_mistral': 2091, 'n_tokens_neox': 1616, 'n_words': 363}