LigParGenForceFieldSource

class propertyestimator.forcefield.LigParGenForceFieldSource(preferred_charge_model=<ChargeModel.CM1A_1_14_LBCC: '1.14*CM1A-LBCC'>, cutoff=<Quantity(9.0, 'angstrom')>)[source]

A wrapper and the OPLSAAM force field which can be applied via the LigParGen server.

References

[1] Potential energy functions for atomic-level simulations of water and organic and

biomolecular systems. Jorgensen, W. L.; Tirado-Rives, J. Proc. Nat. Acad. Sci. USA 2005, 102, 6665-6670

[2] 1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase

Simulations. Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B, 2017, 121 (15), pp 3864-3870

[3] LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands.

Dodda, L. S.;Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L. Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331-W336

__init__(preferred_charge_model=<ChargeModel.CM1A_1_14_LBCC: '1.14*CM1A-LBCC'>, cutoff=<Quantity(9.0, 'angstrom')>)[source]

Constructs a new LigParGenForceFieldSource object

Parameters
  • preferred_charge_model (ChargeModel) – The preferred charge model to apply. In some cases the preferred charge model may not be applicable (e.g. 1.14*CM1A-LBCC may only be applied to neutral molecules) and so another model may be applied in its place.

  • cutoff (unit.Quantity) – The non-bonded interaction cutoff.

Methods

__init__([preferred_charge_model, cutoff])

Constructs a new LigParGenForceFieldSource object

json()

Creates a JSON representation of this class.

parse_json(string_contents[, encoding])

Parses a typed json string into the corresponding class structure.

Attributes

cutoff

The non-bonded interaction cutoff.

preferred_charge_model

The preferred charge model to apply.

class ChargeModel[source]

An enumeration.

property preferred_charge_model

The preferred charge model to apply. In some cases the preferred charge model may not be applicable (e.g. 1.14*CM1A-LBCC may only be applied to neutral molecules) and so another model may be applied in its place.

Type

ChargeModel

property cutoff

The non-bonded interaction cutoff.

Type

unit.Quantity

json()

Creates a JSON representation of this class.

Returns

The JSON representation of this class.

Return type

str

classmethod parse_json(string_contents, encoding='utf8')

Parses a typed json string into the corresponding class structure.

Parameters
  • string_contents (str or bytes) – The typed json string.

  • encoding (str) – The encoding of the string_contents.

Returns

The parsed class.

Return type

Any