Enum: SetupTool¶

Tool used to setup a system for simulation.

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

Permissible Values¶

Value	Meaning	Description
pdb4amber	None	Helps in preparing pdb-format files coming from other places to be compatible…
prepareforleap	None	An action inside cpptraj, that also helps make pdb-format files compatible wi…
packmol	None	PACKMOL creates an initial point for molecular dynamics simulations by packin…
packmol_memgen	None	Packmol-memgen provides a way to generate membrane systems, with or without p…
LEaP	None	The primary program to create a new system in Amber, or to modify existing sy…
antechamber	None	The main program to develop force fields for small organic molecules using a …
pyMSMT	None	A way to build, prototype and validate MM models of metalloproteins and organ…
mdgx	None	Allows the generation of bonded force field parameters for any molecule by fi…
parmed	None	Provides a way to extract information about parameters defined in a parameter…

Slots¶

Name	Description
setup_tool	Name of the tool used to setup simulation

Identifier and Mapping Information¶

Schema Source¶

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

LinkML Source¶

name: SetupTool
description: Tool used to setup a system for simulation.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  pdb4amber:
    text: pdb4amber
    description: Helps in preparing pdb-format files coming from other places to be
      compatible with LEaP.
  prepareforleap:
    text: prepareforleap
    description: An action inside cpptraj, that also helps make pdb-format files compatible
      with LEaP. It is particularly useful for carbohydrates.
  packmol:
    text: packmol
    description: PACKMOL creates an initial point for molecular dynamics simulations
      by packing molecules in defined regions of space.
  packmol_memgen:
    text: packmol_memgen
    description: Packmol-memgen provides a way to generate membrane systems, with
      or without protein, by orienting input proteins with Memembed and using Packmol
      as the packing engine.
  LEaP:
    text: LEaP
    description: The primary program to create a new system in Amber, or to modify
      existing systems.
  antechamber:
    text: antechamber
    description: The main program to develop force fields for small organic molecules
      using a version of the general Amber force field (GAFF).
  pyMSMT:
    text: pyMSMT
    description: A way to build, prototype and validate MM models of metalloproteins
      and organometallic compounds.
  mdgx:
    text: mdgx
    description: Allows the generation of bonded force field parameters for any molecule
      by fitting to quantum data.
  parmed:
    text: parmed
    description: Provides a way to extract information about parameters defined in
      a parameter-topology file.