aquaPELE parameters

These are parameters to set up the aquaPELE algorithm within a PELE simulation.

List of aquaPELE parameters:

List of examples:

n_waters

  • Description: Number of new water molecules that will be included into the system and perturbed with aquaPELE. New water molecules will be contained and perturbed inside the water perturbation box that is defined.

  • Type: Integer

  • Default: 0

Note

Note the difference between n_waters and waters. The former is able to introduce new water molecules into the system before initializing the simulation. The latter will not add new water molecules but it will perturb those that are already in the input structure.

See also

Example 1

waters

  • Description: Water molecules to be perturbed with aquaPELE. They must belong to the input structure that is supplied to the Platform. Water molecules must be selected by supplying their chain and residue number. For example, “W:15” will select the water molecule from chain “W” and with residue number 15. All water molecules present in the system can be automatically selected with "all_waters".

  • Type: list of String

  • Default: None

Note

Note the difference between n_waters and waters. The former is able to introduce new water molecules into the system before initializing the simulation. The latter will not add new water molecules but it will perturb those that are already in the input structure.

See also

Example 2

box_water

  • Description: Perturbation box in which water molecules will be perturbed with aquaPELE.

  • Type: 3-dimensional array of Float

  • Default: center of mass of all water molecules to perturb

Note

Note that aquaPELE’s box can only be spherical.

See also

Example 1

water_radius

  • Description: Radius, in angstroms, for the perturbation box in which water molecules will be perturbed with aquaPELE.

  • Type: Float

  • Default: 7

Note

Note that aquaPELE’s box can only be spherical.

See also

Example 1

water_temp

  • Description: Temperature, in Kelvin, for the internal Metropolis criterion of aquaPELE. The higher it is, the easier it is to accept new water locations, even if they increase the energy of the system. Thus, the higher it is the harder it is to accept the new state of the system at the end of the PELE step by the outer Metropolis criterion. However, a high temperature promotes the sampling of water molecules.

  • Type: Float

  • Default: 5000

Note

Note the difference between temperature and water_temp. The former affects the global Metropolis criterion that is applied at the end of each PELE step and decides if we accept or reject the new state of the system. The latter only affects the internal Metropolis criterion of aquaPELE which is in charge of accepting or rejecting each water move.

See also

temperature, Example 1

Example 1

In this example we set an induced fit docking simulation with 30 computation cores. Moreover, we add 2 new water molecules inside the water box that we define. Specifically, the spherical box we define is centered at (15, -2, 9) and has a radius of 8 angstroms. Finally we set a temperature for the Metropolis criterion of aquaPELE equal to 7000 Kelvin.

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# aquaPELE parameters
n_waters: 2
box_water:
  - 15
  - -2
  - 9
water_radius: 8

Example 2

In this example we set an induced fit docking simulation with 30 computation cores. Moreover, we select 3 water molecules from the input structure to be perturbed with aquaPELE.

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# aquaPELE parameters
waters:
  - "W:1"
  - "W:3"
  - "W:10"