MoleculeImporter

class AmberFD.AmberFD.MoleculeImporter(ff_files, structure_files, solvate=False, **solvate_kwargs)
__init__(ff_files, structure_files, solvate=False, **solvate_kwargs) → None

Loads multiple molecule files at once and stores the positions, topology, and forcefield information into one object. MoleculeImporter can also solvate the system, using all valid solvation options that are used in openmm.app.modeller.addSolvent()

Parameters

  • ff_files (tuple or string) – The .xml OpenMM forcefield files to use

  • structure_files (tuple or string) – Molecule files to load, depending on the type. If using a .pdb file, only one file needs to be supplied. If using GROMACS files, then a tuple of (.gro, .top) files should be used

  • solvate (bool) – Whether or not to solvate the system. This is controlled using the following solvent_kwargs, which take on the same options used to solvate the system that are used with openmm.app.modeller.addSolvent(). However, the kward ‘forcefield’ will be ignored: instead, force field files used with the ‘ff_files’ option will be used.

Keyword Arguments

  • model (str='tip3p') – the water model to use. Supported values are ‘tip3p’, ‘spce’, ‘tip4pew’, and ‘tip5p’.

  • boxSize (Vec3=None) – the size of the box to fill with water

  • boxVectors (tuple of Vec3=None) – the vectors defining the periodic box to fill with water

  • padding (distance=None) – the padding distance to use

  • numAdded (int=None) – the total number of molecules (waters and ions) to add

  • positiveIon (string='Na+') – the type of positive ion to add. Allowed values are ‘Cs+’, ‘K+’, ‘Li+’, ‘Na+’, and ‘Rb+’

  • negativeIon (string='Cl-') – the type of negative ion to add. Allowed values are ‘Cl-’, ‘Br-’, ‘F-’, and ‘I-’. Be aware that not all force fields support all ion types.

  • ionicStrength (concentration=0*molar) – the total concentration of ions (both positive and negative) to add. This does not include ions that are added to neutralize the system. Note that only monovalent ions are currently supported.

  • neutralize (bool=True) – whether to add ions to neutralize the system

Methods

__init__(ff_files, structure_files[, solvate])

Loads multiple molecule files at once and stores the positions, topology, and forcefield information into one object.