Absolute Binding of Host cucurbit[7]uril with Guest molecule B2 in Implicit Solvent

This example illustrates the computation of the binding free energy of B2 guest to the host cucurbit[7]uril in an NVT non-periodic system of implicit water. From description, we will craft the settings, molecules, and simulations in YANK. This example will be less detailed than the full detailed example of p-xylene and T4 Lysozyme

This example resides in {PYTHON SOURCE DIR}/share/yank/examples/binding/host-guest. The rest of the example here assumes you are in this directory.

This example and files are based on this AMBER tutorial.

Examining YAML file

Here we will look at the YAML file and options relevant to this run. We assume you have looked at the detailed p-xylene in T4 Lysozyme example for a more detailed explanation of the YAML file and the settings.

Options Heading

options:
  minimize: yes
  verbose: yes
  number_of_iterations: 500
  temperature: 300*kelvin
  pressure: null
  output_dir: hgoutput

We choose to minimize the simulation to reduce the chance of an unstable starting configuration. Then set verbose to see what is happening.

We will be running implicit, non-periodic NVT system. So we set the temperature, then set the pressure to null to ensure we are in NVT mode.

Finally, we set a limited number of iterations with number_of_iterations (for this example) and choose a specific output directory called hgoutput. Note that this folder is relative to the yank.yaml file.

Molecules Heading

molecules:
  cucurbit:
    filepath: setup/host.tripos.mol2
    leap:
      parameters: leaprc.gaff2
    antechhamber:
      charge_method: null
  B2:
    filepath: setup/guest.tripos.mol2
    antechamber:
      charge_method: bcc

Both molecules in this example are mol2 files, however, there are some nuances.

The host file has charges pre-assigned to it, but the gaff2 force field does not know the atom names that are in the file. We pre-assign charges to molecules as the charge assignment process can be rather taxing for large molecules, and YANK would have to do it every start up unless molecule preparation was already done, and resume_simulation is set to yes. On this host/guest system, the process would not take long, but in general, large molecules should be pre-assigned charge. Normally, simply naming the file with filepath would be sufficient, but since we are missing parameters in GAFF, we still invoke antechamber. Note though, the charge_method is set to null so we don’t attempt to re-assign charges.

The guest molecule, B2, is identical to earlier examples and no further options are needed.

Solvents Heading

solvents:
  GBSA:
    nonbonded_method: NoCutoff
    implicit_solvent: OBC2

The solvent in this case is an implicit/continuum dielectric solvent. We choose the options NoCutoff to mean that all particle interactions are computed without any kind of cutoff, without periodic copes. Because there are significantly fewer atoms in this system, we use NoCutoff to be as accurate as possible without taking too much computational effort.

We set implicit_solvent to tell YANK to actually a continuum solvent. If we had not set this, we would have gotten a solvent representing a vacuum. The argument given to implicit_solvent is linked to OpenMM’s implicit solvent names. In this case, the OBC2 name is the Onufriev-Bashford-Case GBSA model. We could change the dielectric, but YANK defaults to the dielectric for TIP3P water.

Systems and Protocols Headings

The headings systems and protocols are straightforward. Please see the more detailed p-xylene in T4 Lysozyme example for more information on these sections.

Note however in the protocols heading there is not a lambda_restraints specified, the reason for that is the type of restraint we choose as we discuss below.

Experiments Heading

experiments:
  system: host-guest
  protocol: absolute-binding
  restraint:
    type: FlatBottom

This experiments heading differs from the p-xylene binding example due to the type of restraint we chose, in this case, FlatBottom.

We apply a FlatBottom restraint to keep the guest from wondering too far away from the host. The FlatBottom option applies no biasing potential until the guest drifts too far away at which point a harmonic bias is applied relative to the geometric center of the host. It loosely follows this equation:

\[\begin{split}U_{\text{restraint}}(r) = \begin{cases} 0 & \,\text{if}\, r \le r_{\text{cutoff}} \\ K \cdot \left(r-r_{\text{cutoff}} \right)^2 & \,\text{if}\, r > r_{\text{cutoff}} \end{cases}\end{split}\]

The Flat Bottom restraint has another advantage on this system in particular. The symmetric host molecule is known to have multiple binding sites that are hard to locate in normal simulation time lengths. The FlatBottom restraint allows the guest to explore more of the space around the host relative to the other restraint type Harmonic.

The Harmonic restraint type would keep the ligand close to the centroid of the host, which may only favor one of the bindning sites. It should be noted though, that if you want to keep the close to a the centroid, the Harmonic restraint may be a better option. We do this in the p-xylene binding example since the binding site is close to the centroid of the receptor and the Harmonic restraint is not so strong as to overcome natural kinetic barriers.

We also note that we did not specify lambda_restraints because we want every state to take the same and default value of 1.0. This differs from the p-xylene binding example because we want the ligand to explore the simulation box, without drifting too far away.

Running and Analyzing the Simulation

The execution and analysis of the simulation are handled the same as in the T4 Lysozyme binding example. Please see the documentation on that page for more information.