Department of Chemistry, Faculty of Science, University of Kurdistan

AMBER

AMBER (Assisted Model Building with Energy Refinement) is a program suite for biomolecular simulations [1]. Its project began in the late 1970s and has been maintained by an active development community. It is a powerful tool for performing molecular mechanics (MM) optimizations and molecular dynamics (MD) simulations. AMBER can be used to perform other types of classical calculations, such as MM-PBSA and MM-GBSA, to estimate ligand-binding affinities.

Official Homepage: https://ambermd.org/

1. Installation by Javad Shirazi

The following is an explanation of how to install Amber22 on Ubuntu 22.10. However, it may also work with other versions of Ubuntu. It is possible to perform most classical calculations using AmberTools, which is a free program. However, more sophisticated and faster AMBER modules (pmemd and its GPU accelerated version, pmemd.cuda) are not included in AmberTools. It is necessary to purchase the AMBER program to use these modules. There is, however, a waiver option available from the ABMER group for scientists who are not based in North America, Western Europe, or Japan. Visit the official AMBER website for more information.

1.1 Install cmake and a few other necessary packages

Switch to the root user and install cmake and a few other necessary packages

sudo su

apt update

apt upgrade

apt install cmake

apt -y update

apt -y install tcsh make

apt install gcc

apt -y install gcc gfortran

apt -y install flex bison patch

apt -y install bc xorg-dev libbz2-dev wget

apt-get install gcc build-essential

1.2 Make a subdirectory in your /opt directory (e.g., 'amber') in the root environment

cd /opt

mkdir amber

cd amber/

1.3 Copy the AmberTools22.tar.bz2 and Amber22.tar.bz2 files into the 'amber' directory.

You can download them from https://ambermd.org/GetAmber.php or copy them from a local system. We use the following command to copy them from a local machine).

scp mehdi@172.16.13.126:/home/mehdi/AMBER22/Amber* .

1.4 Extract the AmberTools22.tar.bz2 and Amber22.tar.bz2 files

tar xvjf AmberTools22.tar.bz2

tar xvfj Amber22.tar.bz2

Note that, both Amber22 and AmberTools22 should be extracted into the same directory tree, whose head will be 'amber22_src'. If you do not have the Amber22.tar.bz2 file or do not unpack it, the pmemd module will not be installed. However, you will be able to use all other modules, especially sander, which is a proper alternative for running MD simulations.

1.5 Compile and install AMBER

cd /opt/amber/amber22_src/build

./run_cmake

If this does not work, install a few other necessary packages as follows.

sudo apt install pip

pip install numpy

python3 -m pip install scipy

pip install Cython

pip install setuptools

python3 setup.py install

pip install tk

python3 -m pip install -U pip

pip install matplotlib

sudo apt install python3-tk

There are two lines like the following in the run_cmake file in the build subdirectory. Set DOWNLOAD_MINICONDA to FALSE, and let CMake find your Python interpreter on the PATH. This has to be done after the installation of the above packages. After that rerun cmake as follows.

./run_cmake

Finally, execute the following commands.

make install

source /opt/amber/amber22/amber.sh

1.6 Insert the AMBER path into your .bashrc file

echo '#AMBER' >> ~/.bashrc

echo 'source /opt/amber/amber22/amber.sh' >> ~/.bashrc

1.7 Parallelization of AMBER

To run the AMBER program on more than one CPU core, execute the following commands.

apt -y install openmpi-bin libopenmpi-dev openssh-client

cd /opt/amber/amber22_src/AmberTools/src

wget www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz

tar vxzf mpich-3.3.2.tar.gz

./configure_mpich gnu

cd ../../build

There are two lines like the following in the run_cmake file in the build subdirectory. Change '-DMPI=FALSE' to '-DMPI=TRUE' in the second line. You may use the vi text editor to do this. Then recompile the program.

./run_cmake

make install

source /opt/amber/amber22/amber.sh

2. Activate the AMBER program to desired accounts on your local machine

2.1 Add a group and name it 'amber'.

groupadd -g 3333 amber

2.2 Add your user ID to the amber group

In the following command, 'mehdi' is my user-id.

usermod -a -G amber mehdi

2.3 Change the permission and owner of the orca directory

In the following, 3333 is the orca group id that we created in step ‎‎2.2.

cd /opt

chown -R root:3333 amber

chmod -R 750 amber

2.4 Switch to your user and insert the path of AMBER into your .bashrc file

su mehdi

echo '#Abmer22' >> ~/.bashrc

echo ' source /opt/amber/amber22/amber.sh' >> ~/.bashrc

source ~/.bashrc

3. References

[1] D.A. Case, T.E. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, A. Onufriev, C. Simmerling, B. Wang, R.J. Woods, The Amber biomolecular simulation programs, J. Comput. Chem. 26 (2005) 1668–1688. https://doi.org/10.1002/jcc.20290.