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biobb_amber

Introduction

biobb_amber is a BioBB category for AMBER MD package. biobb_amber allows setup and simulation of atomistic MD simulations using AMBER MD package and its associated AMBER tools. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v4.2.0 2024.1

Installation

Using PIP:

Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA or DOCKER.

Using ANACONDA:

Using DOCKER:

  • Installation:

      docker pull quay.io/biocontainers/biobb_amber:4.2.0--pyhdfd78af_0
    
  • Usage:

      docker run quay.io/biocontainers/biobb_amber:4.2.0--pyhdfd78af_0
    

Using SINGULARITY:

MacOS users: it’s strongly recommended to avoid Singularity and use Docker as containerization system.

  • Installation:

      singularity pull --name biobb_amber.sif https://depot.galaxyproject.org/singularity/biobb_amber:4.2.0--pyhdfd78af_0
    
  • Usage:

      singularity exec biobb_amber.sif <command>
    

The command list and specification can be found at the Command Line documentation.