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/
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 usingAmberTools, which is a free program. However, more sophisticated and faster AMBER modules (pmemdand its GPU accelerated version,pmemd.cuda) are not included inAmberTools. 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 officialAMBER websitefor more information.
1.1Installcmakeand a few other necessary packages
Switch to the root user and installcmakeand 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
1.2Make a subdirectory in your /optdirectory (e.g., 'amber') in the root environment
cd /opt
mkdir amber
cd amber/
1.3Copy theAmberTools22.tar.bz2andAmber22.tar.bz2files into the 'amber' directory.
You can download them fromhttps://ambermd.org/GetAmber.phpor copy them from a local system. We use the following command to copy them from a local machine).
[email protected]:/home/mehdi/AMBER22/Amber*.
1.4Extract theAmberTools22.tar.bz2andAmber22.tar.bz2files
tar xvjfAmberTools22.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 theAmber22.tar.bz2file or do not unpack it, thepmemdmodule will not be installed. However, you will be able to use all other modules, especiallysander,which is a proper alternative for runningMD simulations.
1.5Compile 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 therun_cmakefile in the build subdirectory. SetDOWNLOAD_MINICONDAtoFALSE, and letCMakefind your Python interpreter on the PATH. This has to be done after the installation of the above packages. After that reruncmakeas follows.
./run_cmake
Finally, execute the following commands.
make install
source /opt/amber/amber22/amber.sh
1.6Insert the AMBER path into your .bashrcfile
echo '#AMBER' >> ~/.bashrc
echo 'source /opt/amber/amber22/amber.sh'>>~/.bashrc
1.7Parallelization ofAMBER
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 therun_cmakefile in thebuildsubdirectory. Change '-DMPI=FALSE' to '-DMPI=TRUE' in the second line. You may use thevitexteditor to do this. Then recompile the program.
./run_cmake
make install
source /opt/amber/amber22/amber.sh
2.1Add a group and name it 'amber'.
groupadd-g3333amber
2.2Add your user ID to theambergroup
In the following command, 'mehdi' is my user-id.
usermod-a-Gambermehdi
2.3Change the permission and owner of the orca directory
In the following, 3333 is the orca group id that we created in step2.2.
cd/opt
chown-Rroot:3333amber
chmod-R750amber
2.4Switch to your user and insert the path of AMBER into your .bashrcfile
su mehdi
cd
echo '#Abmer22'>> ~/.bashrc
echo ' source /opt/amber/amber22/amber.sh'>> ~/.bashrc
source ~/.bashrc
[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.
