Residue parametrization

These are parameters to manage the parametrization of residues. For a complete guide on the parameters that PELE needs in order to run successfully, check the Custom template generation documentation.

List of ligand parameters:

List of examples:

use_peleffy

  • Description: Activates peleffy instead of the default parameters builder.

  • Type: Boolean

  • Default: False

Warning

Although it is still not the default option, peleffy will soon be the default option to parametrize non standard residues.

Note

Note that the usage of any OpenFF force field requires activating peleffy.

Note

To get more information about peleffy you can check its specific documentation

or one of our tutorials.

See also

peleffy tutorial, forcefield, Example 1, Example 2, Example 4

templates

  • Description: Sets a list of external templates. Templates are files containing the parameters of the force field corresponding to a specific residue. Check this page to get further information.

  • Type: list of String

  • Default: None

Warning

Double check that all atoms in the template match with those in the input structure of PELE for all involved residues. In case that PELE finds any mismatch between these files, it will raise an exception with information about any non matching atom that is found. To solve these problems, read carefully PELE messages and verify the parametrization process.

Note

Any residue parametrized in one of the external templates supplied with this flag will not be parametrized with our internal parametrization workflow.

See also

rotamers, solvent_template, Example 3, Example 4

rotamers

  • Description: Sets a list of rotamer libraries. Rotamer libraries are files containing the list of rotatable bonds of a residue arranged by rotatable branches. Check this page to get further information.

  • Type: list of String

  • Default: None

Warning

When the template of a residue is externally supplied with templates option, the internal parametrization workflow skips the preparation of that residue. In order to account for its rotamers, you must also supply them through an external file as they will not be automatically generated.

See also

templates, solvent_template, Example 3, Example 4

solvent_template

  • Description: Sets a list of solvent templates. Solvent templates are files containing the solvent parameters of a residue. Check this page to get further information.

  • Type: list of String

  • Default: None

Warning

When the template of a residue is externally supplied with templates option, the internal parametrization workflow skips the preparation of that residue. In order to correctly set its solvent parameters, you must also supply them through an external file as they will not be automatically generated.

Note

Solvent templates are only required when the OBC solvent model is used.

See also

templates, rotamers, solvent, Example 3, Example 4

Example 1

In this example we set an induced fit docking simulation with 30 computation cores. We also activate peleffy and use the latest OpenFF force field to parametrize non standard residues.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# PELE parameters
forcefield: "openff-2.0.0"

# Parametrization parameters
use_peleffy: True

Example 2

In this example we set an induced fit docking simulation with 30 computation cores. We also activate peleffy and use the OPLS2005 force field to parametrize non standard residues.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# PELE parameters
forcefield: "OPLS2005"

# Parametrization parameters
use_peleffy: True

Example 3

In this example we set an induced fit docking simulation with 30 computation cores. We are using the default force field, which is OPLS2005. However, in this case, we supply custom templates for our ligand. These files can be generated externally with peleffy.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# Parametrization parameters
templates:
    - "simulation_files/ligz"
rotamers:
    - "simulation_files/LIG.rot.assign"

Example 4

In this example we set an induced fit docking simulation with 30 computation cores. We are using the latest OpenFF force field, which works with the OBC solvent model. So, in this case, if we supply custom templates for our ligand we also need to supply the solvent template. These files can be generated externally with peleffy.

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

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# PELE parameters
forcefield: "openff-2.0.0"

# Parametrization parameters
use_peleffy: True
templates:
  - "simulation_files/ligz"
rotamers:
  - "simulation_files/LIG.rot.assign"
solvent_template:
  - "simulation_files/ligandParams.txt"