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AmberTools 17

AmberTools provides ptraj, reduce, tleap and other packages wrapped by Biskit
  1. Download AmberTools from http://ambermd.org/#AmberTools

  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'
    
  3. Configure AMBERHOME environment variable and include amber binaries in PATH

    add the following to your .bashrc or .zshenv or similar shell startup script:

    export AMBERHOME=/opt/amber16  ## for zsh or bash;
    export PATH="${PATH}:${AMBERHOME}/bin"
    

    Note:

    Alternatively, you can include the amber.sh file created by the Amber configure script below using a source statement: source /opt/amber16/amber.sh

  4. Install dependencies for compilation

    standard needs on Ubuntu / Debian:

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

    Note:

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

    optional: dependencies for MPI parallelization:

    sudo apt-get install openmpi-bin libopenmpi-dev
    
  5. Configure AmberTools:

    cd $AMBERHOME
    sudo ./configure gnu
    source /opt/amber16/amber.sh
    

    Note

    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.

  6. Compile:

    sudo make install
    

    Note

    Repeat step 5 substituting 'configure -mpi gnu' and then 6 for the compilation of parallelized versions.

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:

    python reduce.py
    
  2. tleap:

    python AmberParmBuilder.py
    
    python AmberLeap.py
    
  3. cpptraj:

    python AmberCrdEntropist.py
    
    python AmberEntropist.py