Enum: NucleicPotentialName

Force fields used to parametrize nucleic acids in a simulation.

URI: https://CCPBioSim.ac.uk/biosim-schema/NucleicPotentialName

Permissible Values

Value	Meaning	Description
ff99-bsc0	None	Force field for nucliec acids
ff99OL3	None	Force field for RNA, where quantum mechanics methods at various levels were e…
LJbb	None	RNA force field with modified phosphate parameters (from OL force field) and …
ROC	None	Force field with alternative set of torsions for RNA, fit to quantum calculat…
Shaw	None	RNA force field with more extensive modifications
OL15	None	Force field for DNA, with a combination of three dihedral updates
OL21	None	DNA force field that adds some new torsion modifications, aimed at non-B doub…
OL24	None	OL24 is a 2024 DNA force field tested on both canonical and non-canonical DNA
OL3	None	The Amber OL3 force field is a parameter set for simulations of RNA
bsc1	None	Updated version of bsc0 force field for DNA, using an implicit solvation mode…
terminal_monophosphate	None	Force field library for the 5\’ end of many DNA and RNA chains have one or mo…

Slots

Name	Description
nucleic_potential_name	Force field used to describe nucleic acids

Identifier and Mapping Information

Schema Source

• from schema: https://CCPBioSim.ac.uk/biosim-schema/

LinkML Source

name: NucleicPotentialName
description: Force fields used to parametrize nucleic acids in a simulation.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  ff99-bsc0:
    text: ff99-bsc0
    description: Force field for nucliec acids. High level quantum mechanics calculations
      were perfomed on models of sugars and phosphates, specifically a sugar-phosphate
      model and a sugar-phosphate-sugar model.
  ff99OL3:
    text: ff99OL3
    description: Force field for RNA, where quantum mechanics methods at various levels
      were employed to improve the chi angle distribution using relevant model systems.
  LJbb:
    text: LJbb
    description: RNA force field with modified phosphate parameters (from OL force
      field) and an improved water model (OPC), which has better agreement with NMR
      data for RNA tetranucleotide populations.
  ROC:
    text: ROC
    description: Force field with alternative set of torsions for RNA, fit to quantum
      calculations.
  Shaw:
    text: Shaw
    description: RNA force field with more extensive modifications.
  OL15:
    text: OL15
    description: Force field for DNA, with a combination of three dihedral updates.
  OL21:
    text: OL21
    description: DNA force field that adds some new torsion modifications, aimed at
      non-B double helices, as of Amber24, is the current recommended DNA force field.
  OL24:
    text: OL24
    description: OL24 is a 2024 DNA force field tested on both canonical and non-canonical
      DNA.
  OL3:
    text: OL3
    description: The Amber OL3 force field is a parameter set for simulations of RNA.
  bsc1:
    text: bsc1
    description: Updated version of bsc0 force field for DNA, using an implicit solvation
      model and a rigorous quantum mechanics methodology.
  terminal_monophosphate:
    text: terminal_monophosphate
    description: Force field library for the 5\’ end of many DNA and RNA chains have
      one or more phosphate groups.