PELE metrics

These are parameters to manage the metrics that PELE needs to track during the simulation.

List of metric-related parameters:

List of examples:

atom_dist

  • Description: Asks for the distance calculation between pairs of atoms during the PELE simulation. More than one pair of atoms can be appended to the list if more than one atomic distance must be retrieved.

  • Type: list of Character:Integer:String````Integer

  • Default: None

See also

rmsd_pdb, Example 1, Example 2

rmsd_pdb

  • Description: Defines the path to a PDB structure that will be used to calculate the RMSD of the ligand during the PELE simulation.

  • Type: String

  • Default: None

Note

Note that the PDB structure supplied as a reference must be aligned to the input structure prior to the simulation. Additionally, it must contain the same ligand with matching residue name, residue number and PDB atom names.

See also

atom_dist, Example 1

Example 1

In this example we set an induced fit docking simulation with 30 computation cores. We also ask for the calculation of a distance between two atoms and the RMSD of the ligand with respect to a reference structure.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# PELE metrics parameters
atom_dist:
    - "A:2:CA"
    - "B:3:CG"
rmsd_pdb: "reference.pdb"

Example 2

In this example we set an induced fit docking simulation with 30 computation cores. We also ask for the calculation of two distances between atoms A:2:CA and B:3:CG, and also between A:5:N and B:3:CG.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# PELE metrics parameters
atom_dist:
    - "A:2:CA"
    - "B:3:CG"
    - "A:5:N"
    - "B:3:CG"