Cookbook for YAML Options¶

Having all the options laid out in front of you is good for advanced users, but sometimes practical examples are much more helpful. Below is the YANK YAML Cookbook: A series of examples that may help you understanding how to put together the options found on the other pages.

Best Practices Shown by These Examples¶

The following examples exemplify some of the best practices laid out on alchemistry.org. Specifically:

There are no partial atomic charges on an atom while its Lennard-Jones interactions are being removed.
The whole free energy setup and run is automated through YANK’s YAML format, meaning its easily transferable and repeatable
A statistically efficient alchemical path is selected because the softcore_X parameters were not set, so the default, efficient, soft core parameters were chosen automatically.

Example: Implicit Solvent Binding Simulation:¶

This example sets up para-xylene binding to T4-Lysozyme in implicit solvent. We recommend these settings as a good baseline simulation setup. Although you do not have to set all these options (e.g. the ligand may be a pdb file, not just a SMILES string), many of these options are good stock settings to remember.

In this example:

Targeting folders for input files
Configuring Output files
Setting good stock options for implicit simulations
Setting up simple protein/ligand binding simulation
NVT ensemble

options:
  verbose: yes
  setup_dir: setup
  output_dir: output
  experiments_dir: experiments
  randomize_ligand: yes
  minimize: yes
  number_of_iterations: 2000
  temperature: 300*kelvin
  pressure: null

molecules:
  T4_lysozyme:
    filepath: T4.pdb
  p-xylene:
    smiles: CC1=CC=C(C=C1)C
    antechamber:
      charge_method: bcc

solvents:
  GBSA:
    nonbonded_method: NoCutoff
    implicit_solvent: OBC2
    solvent_dielectric: 78.5

systems:
  T4-xylene-complex:
    receptor: T4_lysozyme
    ligand: p-xylene
    solvent: GBSA
    pack: yes
    leap:
      parameters: [leaprc.ff14SB, leaprc.gaff]

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:
        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]

experiments:
  system: T4-xylene-complex
  protocol: absolute-binding
  restraint:
    type: FlatBottom

After this is all setup, simply run: yank script --yaml={ThisScriptName.yaml} and YANK will take care of the rest for you.

Example: Absolute Binding free energy in explicit solvent¶

This example takes the same para-xylene binding to T4-Lysozyme system as before, but now uses an explicit solvent setup, minimal options, and automatic water addition (TIP3P).

This example also shows how to make YANK run with MPI; assumes 4 nodes are available. It should be noted there is nothing you set in the YAML file or with YANK itself to run with MPI. YANK automatically detects if MPI was called to run YANK and interacts with it accordingly.

In this Example:

Automatic solvent addition
Setting good stock options for explicit simulations
Call MPI
NPT ensemble

 options:
   minimize: yes
   verbose: yes
   output_dir: .
   number_of_iterations: 2000
   temperature: 300*kelvin
   pressure: 1*atmosphere

  molecules:
    t4-lysozyme:
      filepath: setup/receptor.pdbfixer.pdb
      parameters: leaprc.ff14SB
    p-xylene:
      filepath: setup/ligand.tripos.mol2
      antechamber:
        charge_method: bcc

solvents:
  PME:
    nonbonded_method: PME
    nonbonded_cutoff: 0.9*nanometer
    switch_distance: 0.8*nanometer
    clearance: 12*angstroms
    positive_ion: Na+
    negative_ion: Cl-

systems:
  t4-xylene-explicit:
    receptor: t4-lysozyne
    ligand: p-xylene
    solvent: PME
    leap:
      parameters: [leaprc.ff12, leaprc.gaff]

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:
        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]

experiments:
  system: t4-xylene-explicit
  protocol: absolute-binding
  restraint:
    type: Harmonic

Now run:

$ build_mpirun_configfile "yank script --yaml=yank.yaml"
$ mpiexec -f hostfile -configfile configfile

The build_mpirun_configfile is a command available if you have installed YANK through conda, and though the clusterutils repo.