Ligand parameters¶

These are parameters that affect to how the ligand is treated during the PELE simulation. A ligand is a small molecule that PELE perturbs during perturbation stage in the PELE step. Check the PELE algorithm to get further information about it.

List of ligand parameters:

ligand_conformations

List of examples:

Example 1

ligand_conformations¶

Description: Defines the path to the directory containing ligand conformations in PDB format. When it is supplied, the conformation perturbation algorithm will be activated.

Type: String

Default: None

Warning

In order to properly apply these conformations during the PELE simulation, we must ensure that PDB atom names of the simulation input structure (system parameter) match with those defined in the conformations supplied with ligand_conformations parameter.

Note

The path supplied with ligand_conformations parameter must contain several PDB files of the same ligand. They need to include only the ligand which must have exact PDB atom names and atom ordering. They only need to differ from the coordinates of their atoms thereby representing different ligand conformations.

Note

The number of conformations to include will depend on the chemistry and flexibility of the ligand. Typically, 20-30 conformations is a good choice in most cases.

See also

Conformation perturbation, system, conformation_freq, Example 1

Example 1¶

In this example we set an induced fit docking simulation with 30 computation cores. We also provide a path that contains different conformations of our ligand with the ligand_conformations parameter. This option will activate the Conformation perturbation algorithm that adds an extra perturbation step to visit all supplied ligand conformations during the PELE simulation.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# Ligand parameters
ligand_conformations: "LIG_conformations"