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 12.04 or later), the following command should get you the needed packages:

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

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.

A variety of python packages are needed to use MdoutAnalyzer and xparmed.py:

sudo apt-get install python-tk python-dev python-matplotlib python-numpy python-scipy

For the experimental Phenix interface (not yet distributed), you also need boost-python:

sudo apt-get install libboost-python-dev

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

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