AmberTools 17

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
   wget http://ambermd.org/downloads/install_ambertools.sh
   bash install_ambertools.sh --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/amber.sh cannot be "sourced" from other shell scripts to set the Amber environment

2. Prepare Amber Environment

   Instead of source /opt/amber17/amber.sh 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 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' (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
   

   Note:

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

   MacOSX:

   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
   source amber.sh
   sudo make install
   

   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.

   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/amber.sh
   

   Note:

   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:

   python reduce.py
   

2. tleap:

   python AmberParmBuilder.py
   
   python AmberLeap.py
   

3. cpptraj:

   python AmberCrdEntropist.py
   
   python AmberEntropist.py