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

v4.0.1 2023.1

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.

Installation:
```
  pip install "biobb_amber>=4.0.1"
```
Usage: Python API documentation

Using ANACONDA:

Installation:

  conda install -c bioconda "biobb_amber>=4.0.1"

Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation

Using DOCKER:

Installation:

  docker pull quay.io/biocontainers/biobb_amber:4.0.1--pyhdfd78af_0

Usage:

  docker run quay.io/biocontainers/biobb_amber:4.0.1--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:4.0.1--pyhdfd78af_0

Usage:

  singularity exec biobb_amber.sif <command>

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

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).

(c) 2015-2023 Barcelona Supercomputing Center
(c) 2015-2023 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.

Bioexcel