Department of Chemistry, Faculty of Science, University of Kurdistan

AMBER Installation Tutorial and Workshop Handout

AMBER (Assisted Model Building with Energy Refinement) is a suite of programs 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 also perform other classical calculations, such as MM-PBSA and MM-GBSA, to estimate ligand-binding affinities.

· Official Homepage: https://ambermd.org/index.php

In the following sections, we outline a customized installation procedure for AmberTools 25 and Amber24 on Ubuntu Linux. For more details, visit the official AMBER download page and consult Chapter 2 in the AMBER Reference Manual.

· https://ambermd.org/GetAmber.php

· https://ambermd.org/doc12/Amber25.pdf

1. Install CMake and Required Packages

Switch to the root user and install CMake along with the necessary dependencies. If you have sudo privileges, use the following commands:

sudo su

apt update

apt upgrade

apt install cmake

apt -y update

apt -y install tcsh make gcc gfortran flex bison patch bc xorg-dev libbz2-dev wget libz-dev

apt install python-is-python3

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

2. Download AmberTools25 and/or PMEMD24

Download ambertools25.tar.bz2 and pmemd24.tar.bz2 from https://ambermd.org/GetAmber.php into your ~/Downloads directory.

3. Extract files

Move to the /opt directory and extract the tar.bz2 files using the following commands:

cd /opt

tar xvjf /home/mehdi/Downloads/ambertools25.tar.bz2

tar xvfj /home/mehdi/Downloads/pmemd24.tar.bz2

cd /opt

tar xvjf /home/mehdi/Downloads/ambertools25.tar.bz2

# OR: #

tar xvfj /home/mehdi/Downloads/pmemd24.tar.bz2

If you do not have the pmemd24.tar.bz2 file or do not unpack it, you can proceed with the installation, but in the end, you will not be able to use some features of the program. However, you will be able to use the necessary modules that are proper for setting up and running MD simulations.

4. Apply patches

Apply patches to the distribution source files using the update_amber and update_pmemd scripts.

cd /opt/ambertools25_src/

./update_amber --help

./update_amber --update

cd /opt/pmemd24_sr

./update_pmemd --help

./update_pmemd --update

5. Run CMake Script

Run CMake and build the software:

cd /opt/ambertools25_src/build

./run_cmake

make install

6. Add AMBER to .bashrc

Switch to your user and add the AMBER path to your shell configuration file:

echo '#AMBER24' >> ~/.bashrc

echo 'source /opt/ambertools25/amber.sh' >> ~/.bashrc

source ~/.bashrc

7. Activate AMBER for Users

Assign permissions and activate AMBER for users:

groupadd -g 3333 amber

usermod -a -G amber mehdi

cd /opt

chown -R root:3333 ambertools25

chmod -R 750 ambertools25

8. Parallelization (Optional)

To enable parallel execution of AMBER, install MPI and recompile with MPI enabled:

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

cd /opt/amber/amber22_src/AmberTools/src

wget https://www.mpich.org/static/downloads/4.1.1/mpich-4.1.1.tar.gz

tar vxzf mpich-4.1.1.tar.gz

./configure_mpich gnu

cd ../../build

./run_cmake
make install

source /opt/ambertools25/amber.sh

9. 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.