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AmberTools 17

AmberTools provides ptraj, reduce, tleap and other packages wrapped by Biskit

Option 1: Quick-installation of pre-compiled version

The Amber folks provide an installation script that downloads a pre-compiled AmberTools version. This is considerably faster than compilation from source and the final installation occupies less space. We have only tested this on Ubuntu Linux though.

  1. Download and install AmberTools binaries:

    cd /tmp
    bash --prefix /opt --non-conda

    There is a couple of differences to the installation from source described below:

    • AmberTools end up in a folder /opt/amber17 not /opt/amber16
    • /opt/amber17/ cannot be "sourced" from other shell scripts to set the Amber environment
  2. Prepare Amber Environment

    Instead of source /opt/amber17/ include the following commands in your .bashrc or .zshenv or .zshrc or similar shell startup script:

    export AMBERHOME=/opt/amber17
    export PATH=$PATH:$AMBERHOME/bin

Option 2: Compilation from Source (standard route)

  1. Download AmberTools from

  2. Unpack to system-wide location (e.g. /opt or /usr/local/lib):

    cd /opt
    tar xvfj AmberTools17.tar.bz2   ## will create a new folder 'amber16' (not amber17)
  3. Install dependencies for compilation

    standard needs on Ubuntu / Debian:

    sudo apt-get install csh flex patch gfortran g++ make xorg-dev bison libbz2-dev


    additional packages are mentioned in the Amber17.pdf: xorg-dev python-tk python-matplotlib


    You need XCode, XQuartz and gfortran

    optional: dependencies for MPI parallelization:

    sudo apt-get install openmpi-bin libopenmpi-dev
  4. Configure, Compile and Install AmberTools:

    cd /opt/amber16
    sudo ./configure --skip-python gnu
    sudo make install


    Biskit wrappers are not currently using any of the Python interfaces for Amber programs. Things should work regardless whether or not or how you install the Amber python packages.

    For parallelized versions:

    Repeat substituting the configure step for './configure -mpi gnu'

  5. Amber environment configuration

    Add the following line to your shell startup script (that is .bashrc or .zshenv or .zshrc in your home directory):

    source /opt/amber16/


    This will create the $AMBERHOME variable and put all programs in $AMBERHOME/bin into your $PATH.

Testing Biskit / Amber wrappers

Use the Biskit unit testing to verify that Biskit finds all necessary Amber tools. This generally works by executing the biskit python module with the wrapper as a stand-alone script. This will automatically run the build-in test suite for this module in fully verbose mode. The important thing is that there are no errors reported in the end. The last line should be "Run 1 test in y seconds / OK" or very similar.

First change into the Biskit package folder (biskit/Biskit) then execute...

  1. reduce:

  2. tleap:

  3. cpptraj: