autosolvate.multicomponent.MulticomponentSolventBoxBuilder

class autosolvate.multicomponent.MulticomponentSolventBoxBuilder(xyzfile: str, slu_charge=0, slu_spinmult=1, charge_method='resp', slu_count=1, solvent='water', solvent_frcmod='', solvent_off='', solvent_box_name='SLVBOX', slv_generate=False, slv_xyz='', slv_count=1680, cube_size=54, closeness=0.8, folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', outputFile='', water_model: str = 'tip3p', solute_type: str = 'complex', metal_charge: int = 0, total_charge: Any = 'default', chargefile: str = '', qm_kwargs: Dict[str, Any] | None = None, mcpb_kwargs: Dict[str, Any] | None = None, qm_program: str = 'gaussian', qm_exe: str | None = None, qm_dir: str | None = None, nprocs: int = 1, nnodes: int = 1, ncpus: int = 1, srun_use: bool = False, dry_run: bool = False, **kwargs)[source]

Build a solvent box for a single molecule complex as the solute and single solvent

Parameters:

  • xyzfile (str) – structure file of the molecular complex, can be any type within [“xyz”, “pdb”, “mol2”]. “prep”, “lib”, “off” are not supported for molecular complex.

  • slu_charge (int or dict, Optional, default: 0) – Charge of the solute. if complex has charged fragments, provide a dictionary with the three-letter name of the residue as the key and the corresponding charge as the value. If not given, all fragment will be considered as neutral.

  • slu_spinmult (int or dict, Optional, default: 1) – Spin multiplicity of the solute. if complex has non-singlet fragments, provide a dictionary with the three-letter name of the residue as the key and the corresponding charge as the value. If not given, all fragment will be considered as singlet.

  • charge_method (str, Optional, default: “resp”) – name of charge fitting method (bcc, resp)

  • slu_count (int, Optional, default: 1) – number of the solute in the system. Not recommanded to set this parameter. Be cautious about this as the solute may have more than 1 fragments.

  • solvent (str, Optional, default: “water”) – name of the solvent. Predefined solvents include [“water”, “methanol”, “chloroform”, “nma”].

  • solvent_frcmod (str, Optional, default: “”) – path to the frcmod file of the solvent. Required when user have the solvent forcefield parameters prepared.

  • solvent_off (str, Optional, default: “”) – path to the off file of the solvent. Required when user have the solvent forcefield parameters prepared.

  • solvent_box_name (str, Optional, default: “SLVBOX”) – name of the solvent box

  • slv_generate (bool, Optional, default: False) – whether to generate the solvent forcefield parameters with GAFF. If True, the solvent forcefield will be generated with GAFF, where ‘slv_xyz’ parameter will be needed. If False, the solvent will be treated as a predefined solvent in AMBER or user should provide the frcmod & prep files.

  • slv_xyz (str, Optional, default: “”) – path to the xyz file of the solvent. Required when user want to generate the solvent forcefield parameters with GAFF.

  • slv_count (int, Optional, default: 210*8) – number of the solvent in the system.

  • cube_size (int, Optional, default: 54) – size of solvent cube in angstroms

  • closeness (float, Optional, default: 0.8) – Solute-solvent closeness setting, corresponding to the tolerance parameter in packmol in Å,

  • folder (str, Optional, default: current working directory) – the directory where the files are generated

  • outputFile (str, Optional, default: “”) – prefix of the output .pdb, .inpcrd and .prmtop files

  • kwargs (dict) – Other arguments that need to be included in the solute. Remained for future development.

__init__(xyzfile: str, slu_charge=0, slu_spinmult=1, charge_method='resp', slu_count=1, solvent='water', solvent_frcmod='', solvent_off='', solvent_box_name='SLVBOX', slv_generate=False, slv_xyz='', slv_count=1680, cube_size=54, closeness=0.8, folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', outputFile='', water_model: str = 'tip3p', solute_type: str = 'complex', metal_charge: int = 0, total_charge: Any = 'default', chargefile: str = '', qm_kwargs: Dict[str, Any] | None = None, mcpb_kwargs: Dict[str, Any] | None = None, qm_program: str = 'gaussian', qm_exe: str | None = None, qm_dir: str | None = None, nprocs: int = 1, nnodes: int = 1, ncpus: int = 1, srun_use: bool = False, dry_run: bool = False, **kwargs)[source]

Methods

__init__(xyzfile[, slu_charge, ...])

build()

Build the solvated system with molecule complex as the solute and single solvent

get_solvent(solvent[, slv_xyz, ...])