a3fe.run.system_prep

Functionality for running preparation simulations.

Functions

`heat_and_preequil_input`(leg_type, ...)	Heat the input structure from 0 to 298.15 K with GROMACS.
`minimise_input`(leg_type, engine_type, ...)	Minimise the input structure with GROMACS.
`parameterise_input`(leg_type, engine_type, ...)	Paramaterise the input structure, using Open Force Field v.2.0 'Sage' for the ligand, AMBER ff14SB for the protein, and TIP3P for the water.
`run_ensemble_equilibration`(leg_type, ...)	Run the ensemble equilibration for the given leg type.
`run_process`(system, protocol[, work_dir])	Run a process with GROMACS, raising informative errors in the event of a failure.
`solvate_input`(leg_type, engine_type, ...)	Determine an appropriate (rhombic dodecahedron) box size, then solvate the input structure using TIP3P water, adding 150 mM NaCl to the system.

a3fe.run.system_prep.heat_and_preequil_input(leg_type: LegType, engine_type: EngineType, input_dir: str, output_dir: str) → System[source]

Heat the input structure from 0 to 298.15 K with GROMACS.

Parameters:

leg_type (LegType) – The type of the leg.
engine_type (EngineType) – The type of the engine to use for production (GROMACS is always used for preparation.)
input_dir (str) – The path to the input directory, where the required files are located.
output_dir (str) – The path to the output directory, where the files will be saved.

Returns:

preequilibrated_system – Pre-Equilibrated system.

Return type:

_BSS._SireWrappers._system.System

a3fe.run.system_prep.minimise_input(leg_type: LegType, engine_type: EngineType, input_dir: str, output_dir: str) → System[source]

Minimise the input structure with GROMACS.

Parameters:

leg_type (LegType) – The type of the leg.
engine_type (EngineType) – The type of the engine to use for production (GROMACS is always used for preparation.)
input_dir (str) – The path to the input directory, where the required files are located.
output_dir (str) – The path to the output directory, where the files will be saved.

Returns:

minimised_system – Minimised system.

Return type:

_BSS._SireWrappers._system.System

a3fe.run.system_prep.parameterise_input(leg_type: LegType, engine_type: EngineType, input_dir: str, output_dir: str) → System[source]

Paramaterise the input structure, using Open Force Field v.2.0 ‘Sage’ for the ligand, AMBER ff14SB for the protein, and TIP3P for the water. The resulting system is saved to the input directory.

Parameters:

leg_type (LegType) – The type of the leg.
engine_type (EngineType) – The type of the engine to use for production (GROMACS is always used for preparation.)
input_dir (str) – The path to the input directory, where the required files are located.
output_dir (str) – The path to the output directory, where the files will be saved.

Returns:

parameterised_system – Parameterised system.

Return type:

_BSS._SireWrappers._system.System

a3fe.run.system_prep.run_ensemble_equilibration(leg_type: LegType, engine_type: EngineType, input_dir: str, output_dir: str) → None[source]

Run the ensemble equilibration for the given leg type.

Parameters:

leg_type (LegType) – The type of the leg.
engine_type (EngineType) – The type of the engine to use for production (GROMACS is always used for preparation.)
input_dir (str) – The path to the input directory, where the required files are located.
output_dir (str) – The path to the output directory, where the files will be saved.

Return type:

None

a3fe.run.system_prep.solvate_input(leg_type: LegType, engine_type: EngineType, input_dir: str, output_dir: str) → System[source]

Determine an appropriate (rhombic dodecahedron) box size, then solvate the input structure using TIP3P water, adding 150 mM NaCl to the system. The resulting system is saved to the input directory.

Parameters:

leg_type (LegType) – The type of the leg.
engine_type (EngineType) – The type of the engine to use for production (GROMACS is always used for preparation.)
input_dir (str) – The path to the input directory, where the required files are located.
output_dir (str) – The path to the output directory, where the files will be saved.

Returns:

solvated_system – Solvated system.

Return type:

_BSS._SireWrappers._system.System