make-rex.sh

while getopts ":h:g:f:" opt; do
  case ${opt} in
    h ) SUG=$OPTARG
      ;;
    g ) ROC=$OPTARG
      ;;
    f ) YAMLF=$OPTARG
      ;;
    \? ) echo "Usage: make-yaml [-h] [-g] [-f]"
      ;;
  esac
done

cat > "${YAMLF}" <<- _EOT_
options:
  minimize: yes
  verbose: yes
  default_number_of_iterations: 500
  temperature: 300*kelvin
  pressure: 1*atmospheres
  output_dir: output
molecules:
  SUG:
    filepath: ${SUG}
    antechamber: 
      charge_method: bcc
  ROC:
    filepath: ${ROC}
    antechamber:
      charge_method: bcc
solvents:
  GBSA:
    nonbonded_method: NoCutoff 
  pme:
    nonbonded_method: PME
    nonbonded_cutoff: 12*angstroms
    switch_distance: 11*angstroms
    ewald_error_tolerance: 1.0e-4
    clearance: 12*angstroms
    positive_ion: Na+
    negative_ion: Cl-
systems:
  implicit:
    receptor: CB7
    ligand: B2
    solvent: GBSA
    leap:
      parameters: leaprc.gaff2
  explicit:
    receptor: CB7
    ligand: B2
    solvent: pme
    leap:
      parameters: [leaprc.protein.ff14SB, leaprc.gaff, leaprc.water.tip4pew]
protocols:
  absolute-binding:
    complex:
      alchemical_path:
        lambda_electrostatics: [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]
        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, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.15, 0.10, 0.05, 0.00]
    solvent:
      alchemical_path:
        lambda_electrostatics: [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]
        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, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.15, 0.10, 0.05, 0.00]
experiments:
  system: !Combinatorial [implicit, explicit]
  protocol: absolute-binding
  restraint:
    type: Harmonic
_EOT_