Membrane Builder

Create Membrane Builder Project

Let’s walk through how to create a Membrane Builder project. You will need the project ID from a previously created PDB Reader project. For this example, we’ll use the project we just created above.

NOTE: If you don’t include pdbreader_project_id, it will create a membrane-only system.

The following arguments are available for the create_project method:

  • title (str): Project Title

  • ff (str): Project force field type (charmmff, amberff)

  • membrane_type (MembraneType): Membrane type (default: MembraneType.BILAYER)

  • pdbreader_project_id (str | list[str]): The project ID(s) of the PDBreader to be used as solute. - Pass a single str for Bilayer, Nanodisc, Vesicle, Micelle, or HexPhase systems. - Pass a list[str] of 1 or 2 project IDs for a Double Bilayer system (upper/lower leaflet order). - Omit or pass None for a membrane-only system.

  • amberOptions (dict[str, str]): Amber force field options when ff='amberff' (default: None)

Example:

from molcube.membrane_builder.enum import *

# alt: pdbreader_project_id = pdbreader.projectId
pdbreader_project_id = '78080ec8-bfcd-4141-8f22-f0ae805374ff'

# Create Membrane Builder project
mbuilder = molcube.create_membrane_builder_project()
assert mbuilder.create_project(title="my_membrane_project",
   pdbreader_project_id=pdbreader_project_id,
   membrane_type=MembraneType.BILAYER, ff='amberff')

assert mbuilder.align_membrane_protein(option={"align": "ppm"})

You can check the required by the generate_lipid_packing() method for each membrane type using the get_packing_data_form() method.

This method takes the composition_option (str) argument, which can be either ratio or number. (default: ratio)

>>> lipids, box_margin = mbuilder.get_packing_data_form()
lipids Form:
[
  {
    "lipid": "CHL",
    "upRatio": 1,
    "lowRatio": 1
  },
  {
    "lipid": "POPC",
    "upRatio": 4,
    "lowRatio": 4
  }
]

box_margin Form:
{
  "margin": 20
}

# Build lipid packing
assert mbuilder.generate_lipid_packing(lipids, box_margin)

# Replace lipid packing and build system
assert mbuilder.replace_packing()

Finally, we will combine the individual components to build the system for molecular dynamics (MD) simulation. The following arguments are available for the method:

  • waterMargin(float): water margin of Membrane System (default: 22.5).

  • ions (str): Type of ions to use (default: “kcl”).

  • ionConc (float): Ion concentration (default: 0.15).

  • temperature (float): Temperature for the system in Kelvin (default: 310.0).

  • useHmr (bool): Whether to use hydrogen mass repartitioning (default: False).

  • mdEngines (list[str]): Molecular dynamics engine to use (default: [‘openmm’]).

Bilayer additional options:

  • useHydration (bool): Use hydration number method instead of waterMargin (default: False).

  • hydration_number (int): Number of water molecules per one lipid molecule (default: 50).

The available options for ions and mdEngines are as follows:

  • ions / interIons: [‘kcl’, ‘nacl’, ‘cacl2’, ‘mgcl2’]

  • lipaIons / coreIons: [‘cal’, ‘CAL’, ‘mg’, ‘MG’]

  • mdEngines: [‘openmm’, ‘amber’, ‘gromacs’, ‘namd’, ‘genesis’, ‘desmond’]

assert mbuilder.generate_system(ions='kcl', mdEngines=['openmm', 'gromacs'])