MDStudio_amber

The MDStudio Amber services offers a MDStudio WAMP API to the functionality of the Ambertools software package and the small molecule topology generation services powered by the ACPYPE (AnteChamber PYthon Parser interfacE).

Installation Quickstart

MDStudio Amber can be used in the MDStudio environment as Docker container or as standalone service.

Install option 1. Pre-compiled Docker container

MDStudio Amber can be installed quickly from a pre-compiled docker image hosted on DockerHub by:

docker pull mdstudio/mdstudio_amber
docker run (-d) mdstudio/mdstudio_amber

In this mode you will first need to launch the MDStudio environment itself in order for the MDStudio Amber service to connect to it. You can unify this behaviour by adding the MDStudio Amber service to the MDStudio service environment as:

MDStudio/docker-compose.yml:
    
    services:
       mdstudio_amber:
          image: mdstudio/mdstudio_amber
          links:
            - crossbar
          environment:
            - CROSSBAR_HOST=crossbar
          volumes:
            - ${WORKDIR}/mdstudio_amber:/tmp/mdstudio/mdstudio_amber

And optionally add mdstudio_amber to MDStudio/core/auth/settings.dev.yml for automatic authentication and authorization at startup.

Install option 2. custom build Docker container

You can custom build the MDStudio Amber Docker container by cloning the MDStudio_amber GitHub repository and run:

docker build --build-arg AMBER_TOOLS_VERSION=19 MDStudio_amber/ -t mdstudio/mdstudio_amber

The AMBER_TOOLS_VERSION build argument is optional and allows you to choose a different AmberTools version to be installed other then the default version 19. After successful build of the container follow the steps starting from docker run in install option 1.

Install option 3. standalone deployment of the service.

If you prefer a custom installation over a (pre-)build docker container you can clone the MDStudio_amber GitHub repository and install mdstudio_amber locally as:

pip install (-e) mdstudio_amber/

This install requires the AmberTools package to be installed and accessible in your environment using the AMBERHOME environment variable. The acpype script used by the mdstudio_amber package requires the OpenBabel package. After installation ensure that the AMBERHOME environment variable is set and start the service by:

./entry_point_mdstudio_amber.sh

or

export MD_CONFIG_ENVIRONMENTS=dev,docker
python -u -m mdstudio_amber