Side chain perturbation parameters

These are parameters that affect the side chain perturbation algorithm of PELE.

List of PELE general parameters:

List of examples:

covalent_residue

  • Description: Sets chain and residue number of the residue to perturb with the side chain perturbation algorithm.

  • Type: Character:Integer, chain and residue number

  • Default: None

Note

This parameter activates the sidechainPerturbation package. Thus, it is a special case that do not need any further package to be chosen.

See also

perturbation_trials, refinement_angle, packages, Example 1

perturbation_trials

  • Description: Sets the number of trials for the side chain perturbation algorithm.

  • Type: Integer

  • Default: 20

See also

covalent_residue, refinement_angle, packages, Example 1

refinement_angle

  • Description: Sets the refinement angle which affects to the refinement stage. During the refinement, the side chain perturbation algorithm will perform a very soft perturbation, taking random angles between (-refinement_angle, +refinement_angle).

  • Type: Integer

  • Default: 10

See also

covalent_residue, perturbation_trials, packages, Example 1

Example 1

In this example we set a side chain perturbation simulation using 30 computation cores. This simulation will consist on perturbing the side chains of the chosen residue. It can be a standard residue or non standard like an amino acid covalently attached to a small molecule. We also modify the default parameters of the side chain perturbation algorithm, increasing the number of trials and the refinement angle we can achieve more exploration.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
covalent_residue: "A:273"

# Side chain perturbation parameters
perturbation_trials: 12
refinement_angle: 15