autosolvate.multicomponent.MixtureBuilder.add_solute

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

add a solute molecule

Parameters:

  • xyzfile (str) – structure file name, can be any type within [“xyz”, “pdb”, “mol2”]

  • name (str, Optional, default: the base name of the provided structure file) – name of the solute

  • residue_name (str, Optional, default: “SLU”) – residue name of the solute. Note if an mol2 or prep file is provided, the residue name will be read from the file.

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

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

  • number (int, Optional, default: 1) – number of the solute in the system.

  • **kwargs (dict) – additional files needed for the solute, including “mol2”, “frcmod”, “lib”, “prep”, and “off”. 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” and “frcmod” files by adding the following arguments:

    mol2str

    the path of the mol2 file of the solute

    frcmodstr

    the path of the frcmod file of the solute