aiida_amber.cli package

Submodules

aiida_amber.cli.antechamber module

Command line utility to run amber antechamber command with AiiDA.

Usage: aiida_antechamber –help

aiida_amber.cli.antechamber.launch(params)

Run antechamber.

Uses helpers to add amber on localhost to AiiDA on the fly.

• get inputs and outputs

• check if they are files

• add them as nodes

aiida_amber.cli.parmed module

Command line utility to run amber parmed command with AiiDA.

Usage: aiida_parmed –help

aiida_amber.cli.parmed.launch(params)

Run parmed.

Uses helpers to add amber on localhost to AiiDA on the fly.

aiida_amber.cli.pdb4amber module

Command line utility to run amber pdb4amber command with AiiDA.

Usage: aiida_pdb4amber –help

aiida_amber.cli.pdb4amber.launch(params)

Run pdb4amber.

Uses helpers to add amber on localhost to AiiDA on the fly.

aiida_amber.cli.sander module

Command line utility to run amber sander command with AiiDA.

Usage: aiida_sander –help

aiida_amber.cli.sander.launch(params)

Run sander.

Uses helpers to add amber on localhost to AiiDA on the fly.

aiida_amber.cli.tleap module

Command line utility to run amber tleap command with AiiDA.

Usage: aiida_tleap –help

aiida_amber.cli.tleap.launch(params)

Run tleap.

Uses helpers to add amber on localhost to AiiDA on the fly.

• get inputs and outputs

• check if they are files

• add them as nodes

Module contents

aiida_amber

A plugin for using Amber with AiiDA for molecular dymanics simulations.