autosolvate.multicomponent.MulticomponentParamsBuilder

class autosolvate.multicomponent.MulticomponentParamsBuilder(xyzfile: str, name='', residue_name='SLU', charge=0, spinmult=1, charge_method='resp', folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', water_model: str = 'tip3p', **kwargs)[source]

Create amber parameter files for a single xyz or pdb file with multiple separate fragments.

Warning: If you want to create the forcefield for transition metal complexes please use the `boxgen_metal` module instead of `boxgen_multicomponent`.

Parameters:

  • xyzfile (str) – structure file name, can be any structural files that openbabel recognizes.

  • name (array_like, Optional. default: the base name of the provided structure file.)

  • residue_name (array_like, Optional. default: Residue name provided in pdb file or assigned as UAA, UAB, UAC, etc.) – Residue names for each fragments. A list of strings of three capital letters. Its length should equal to the number of fragments in xyzfile. If this parameter is not given, the residues will be assigned by “U” plus “AB”,”AC”,…”AZ”, “BA”…

  • charge (dict | array_like, Optional. default: 0) – Charge for each fragment. A list of integer with its length equal to the number of fragments, or 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.

  • spinmult (dict | array_like, Optional. default: 0) – Multiplicity for each fragment. A list of integer with its length equal to the number of fragments, or 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.

  • outputFile (str, Optional, default=’water_solvated’) – Filename-prefix for outputfiles

  • pre_optimize_fragments (bool, Optional, default: False) – do geometry optimization with MMFF94 forcefield in OpebBabel before running antechamber

  • srun_use (bool, Optional, default=’False) – Run all commands with a srun prefix

  • gaussianexe (str, Optional, default: g16) – name of the Gaussian executeble

  • gaussiandir (str, Optional, default: $GAUSSIANDIR) – path of Gaussian

  • amberhome (str, Optional, default: $AMBERHOME) – path of amber

  • deletefiles (bool, Optional, default: False) – Delete all temporary files except the .prmtop and .inpcrd file of the pdb file provided.

__init__(xyzfile: str, name='', residue_name='SLU', charge=0, spinmult=1, charge_method='resp', folder='/home/docs/checkouts/readthedocs.org/user_builds/autosolvate/checkouts/py312/docs/', water_model: str = 'tip3p', **kwargs)[source]

Methods

__init__(xyzfile[, name, residue_name, ...])

build()