choderalab/yank

options:
  minimize: yes
  verbose: yes
  output_dir: fxr-imp-34
  default_number_of_iterations: 3000
  default_nsteps_per_iteration: 500
  temperature: 300*kelvin
  pressure: null
  default_timestep: 1.5*femtoseconds
  resume_setup: yes
  resume_simulation: yes

molecules:
  Fxr:
    filepath: ../fxr_set2_his_fix.pdb
    strip_protons: yes 
  fxr_LIGAND:
    filepath: ../ligands_set2____FXR_34.mol2
    openeye:
      quacpac: am1-bcc
    antechamber:
      charge_method: null

solvents:
  gbsa:
    nonbonded_method: NoCutoff
    implicit_solvent: OBC2

systems:
  Fxr-ligands:
    receptor: Fxr
    ligand: fxr_LIGAND
    solvent: gbsa
    leap:
      parameters: [leaprc.protein.ff14SB, leaprc.gaff2, leaprc.water.tip3p]

protocols:
  absolute-binding:
    complex:
      alchemical_path:
        lambda_restraints:     [0.00, 0.50, 1.00, 1.00, 1.00]          #, 0.45, 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, 1.000, 1.00, 1.000, 1.00, 1.00]
        lambda_electrostatics: [1.00, 1.00, 1.00, 0.50, 0.00]          #, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 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, 0.000, 0.00, 0.000, 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, 0.95, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.25, 0.20, 0.15, 0.10, 0.075, 0.05, 0.025, 0.01, 0.00]
    solvent:
      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]
        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, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00]

experiments:
  system: Fxr-ligands
  protocol: absolute-binding
  restraint:
    type: Boresch