Installing Amber on Linux

There are "instructions for the impatient": a minimal set of installation instructions, assuming everything works. For more details and explanations, see Jason Swails' wiki.

Installing Amber on Ubuntu Linux

All of Amber will compile and run on Ubuntu Linux platforms (and variants like lubuntu, Kubuntu and xubuntu). For any recent version (say 14.04 or later), the following command should get you the needed packages:

sudo apt-get install csh flex patch gfortran g++ make xorg-dev bison libbz2-dev \
              python-tk python-dev python-matplotlib python-numpy python-scipy

Note: Starting with AmberTools16, you don't need to install the python libraries if you don't wish to: the configure script will offer to download a compatible python for you.

Caution: depending on the graphics hardware (specifically, onboard intel chipsets) and associated drivers for your particular setup, installing the xorg-dev package on Ubuntu has been reported to sometimes also require a reinstall of the xserver (xserver-xorg) and associated machine-dependent 3D acceleration libraries. If you aren't ready to do this, then just configure AMBER with the -noX11 option.

If you want to install Amber in parallel, you can probably use the apt-get versions of MPI:

sudo apt-get install openmpi-bin libopenmpi-dev

Some users might prefer mpich to openmpi. In that case:

sudo apt-get mpich2 libmpich2-dev

If you have trouble with these, go to $AMBERHOME/AmberTools/src, and execute either ./configure_openmpi or ./configure_mpich2.

Installing Amber on Fedora core Linux

Instructions are generally the same as above, except that yum is used as a package manager. The following command should get you the needed libraries:

sudo yum install gcc gcc-gfortran gcc-c++ flex tcsh zlib-devel \
          bzip2-devel libXt-devel libXext-devel libXdmcp-devel python-devel tkinter \
          numpy scipy python-matplotlib openmpi openmpi-devel perl \
          perl-ExtUtils-MakeMaker patch bison
The above should also work on CentOS and Red Hat Enterprise Linux systems as well, although the Python packages may be too outdated to work with Amber. (Starting with AmberTools16, the easiest thing to do is to accept the offer that our configure script will make, and download a version of python known to satisfy our requirements.)

Installing Amber on openSUSE Linux

Instructions are generally the same as above, except that zypper is used as a package manager. The following command should get you the needed libraries:

sudo zypper install gcc gcc-c++ gcc-fortran libtool \
          xorg-x11-devel xorg-x11-libXt-devel libbz2-devel \
          patch python-tk make flex glibc-devel-static python-devel