Constraint parameters

These are parameters to add and modify constraints on the system to simulate with PELE.

List of constraint parameters:

List of examples:

constraint_level

  • Description: Defines the level of constraining the protein backbone. The Platform constraints the backbone through its alpha carbon atoms (CAs). There are different levels of constraints:

    • level 0: no constraints.

    • level 1: terminal CAs constrained with a spring constant of 5 kcal/mol, the rest of the CAs in the backbone with 0.5 kcal/mol at an interval of 10, i.e. every 10 residues.

    • level 2: terminal CAs constrained at 5 kcal/mol, the rest of the CAs with 2.5 kcal/mol at the interval of 8.

    • level 3: the whole backbone is constrained every 5 atoms with 5 kcal/mol.

  • Type: Integer

  • Default: it depends on the package

Note

This parameter is set according to the Platform package that is chosen since it has a strong connection with the type of simulation that is pursued. We strongly suggest relying on the default settings for each package. However, in case of studying a system where the defaults are not optimal (more flexibility or rigidity required), this parameter can be set, and it will prevail over the default settings of any package.

See also

packages, Example 1, Example 2

Example 1

In this example we set an induced fit docking simulation with 30 computation cores. Moreover, we reduce CAs constraints to increase the flexibility of the system. Thus, we set the constraints level to 1. This strategy might be useful when we want to consider the reallocation of some regions of the backbone, such as loops, due to the perturbation of a ligand.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# Constraint parameters
constraint_level: 1

Example 2

In this example we set an out –> in simulation with 50 computation cores to study the entrance of a ligand in the cavity of a GPCR. The best strategy to simulate membrane proteins that lack the membrane is to add strong constraints to the protein backbone. We can set constraint_level to 3 for this purpose.

When using the out –> in package, we also need to set initial and final sites in order to properly define the starting point and the region to explore during the migration of our ligand. Check box parameters to get further information about these two options.

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

# General parameters
cpus: 50
seed: 2021

# Package selection
out_in: True

# Region selection
initial_site: "A:40:CD"
final_site: "A:187:ND2"

# Constraint parameters
constraint_level: 3