The Setup Classes¶
Setup¶
- class amberpy.md_setup.Setup(name, protein_pdb=None, cosolvent=None, simulation_directory='/home/docs/checkouts/readthedocs.org/user_builds/amberpy/checkouts/latest/docs/source')¶
Bases:
object- run_packmol(n_waters=None, n_cosolvents=100, box_size=[50, 50, 50], packmol_input=None)¶
- run_parmed()¶
- run_tleap(box_distance: float = 12.0, box_shape: str = 'box', ions: dict = {'Cl-': 0, 'Na+': 0}, tleap_input: Optional[amberpy.md_setup.TleapInput] = None)¶
Solvates the pdb file and creates paramater/topology and coordinate files for simulation.
- Parameters
box_distance (float) – Minimum distance between the protein and the edge of the water box.
box_shape (str) – Shape of the simulation box. Choose from either ‘box’ (cuboid) or ‘oct’ (truncated octahedron).
ions (dict) – Ions to add to the system. This should be a dictionary where the keys are the ions and the values are the number of ions to add. A value of 0 will attempt to neutralise the system with that ion.
hmr (bool) – Turn on hydrogen mass repartitioning.
tleap_input (TleapInput) – Overrides all other arguments and instead uses a TleapInput instance.
TleapInput¶
- class amberpy.md_setup.TleapInput(protein_forcefield: str = 'ff19SB', water_forcefield: str = 'tip3p', solvate: bool = True, shape: str = 'box', distance: float = 12.0, distance_from_residues: Optional[tuple] = None, ions: dict = {'Cl-': 0, 'Na+': 0}, save_protein: bool = True, ions_rand: bool = True, box_size: Optional[float] = None, no_centre: bool = False, frcmod_list=None, mol2_dict=None)¶
Bases:
objectTleap Input object
- run(pdb, parm7_out, rst7_out, pdb_out=None)¶