autosolvate.multicomponent.MixtureBuilder.add_solvent

MixtureBuilder.add_solvent(xyzfile: str = '', name='', residue_name='SLV', charge=0, spinmult=1, number=1680, **kwargs)[source]

add a type of solvent

Parameters:

  • xyzfile (str) – structure file name, can be any type within [“xyz”, “pdb”, “mol2”, “prep”, “off”]. Can be ignored if the solvent is predefined in AMBER.

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

  • residue_name (str, Optional, default: “SLV”) – residue name of the solvent. Will be ignored if the solvent is predefined in AMBER. This argument will be ignored if a mol2 or prep file is provided together with a frcmod.

  • charge (int, Optional, default: 0) – charge of the solvent

  • spinmult (int, Optional, default: 1) – spin multiplicity of the solvent

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

  • **kwargs (dict) – additional files needed for the solvent, including “mol2”, “frcmod”, “lib”, “prep”, will support “itp”, “top” in the future. If the user want to skip the antechamber and leap steps, the user need to provide the [“mol2” or “prep”] and “frcmod” files by adding the following arguments:

    mol2str

    the path of the mol2 file of the solvent

    frcmodstr

    the path of the frcmod file of the solvent