AMBER

A suite of biomolecular simulation programs, with GPU support and low memory requirements. It provides interface for most quantum chemistry softwares, making it suitable for hybrid QM/QC simulations.

Installed versions

AMBER 22 (default, recommended)

AMBER manual can be downloaded from here: https://ambermd.org/doc12/Amber22.pdf

Submitting an AMBER calculation

This ‘source’ command is needed once per session:

module load amber

This commands is equivalent to:

module load amber/22

Preparing the system for simulation

A minimum set of the AMBER calculatation requires for example initial PDB file (water5.pdb), perparation input (tleap.in) and minimization protocol (minim.in).

An example water5.pdb input:

HETATM    1  O   WAT A   1       0.000   0.000   0.000  1.00  0.00           O
HETATM    2  H1  WAT A   1       0.957   0.000   0.000  1.00  0.00           H
HETATM    3  H2  WAT A   1      -0.239   0.927   0.000  1.00  0.00           H
HETATM    4  O   WAT A   2       3.000   0.000   0.000  1.00  0.00           O
HETATM    5  H1  WAT A   2       3.957   0.000   0.000  1.00  0.00           H
HETATM    6  H2  WAT A   2       2.761   0.927   0.000  1.00  0.00           H
HETATM    7  O   WAT A   3       0.000   3.000   0.000  1.00  0.00           O
HETATM    8  H1  WAT A   3       0.957   3.000   0.000  1.00  0.00           H
HETATM    9  H2  WAT A   3      -0.239   3.927   0.000  1.00  0.00           H
HETATM   10  O   WAT A   4       3.000   3.000   0.000  1.00  0.00           O
HETATM   11  H1  WAT A   4       3.957   3.000   0.000  1.00  0.00           H
HETATM   12  H2  WAT A   4       2.761   3.927   0.000  1.00  0.00           H
HETATM   13  O   WAT A   5       1.500   1.500   2.000  1.00  0.00           O
HETATM   14  H1  WAT A   5       2.457   1.500   2.000  1.00  0.00           H
HETATM   15  H2  WAT A   5       1.261   2.427   2.000  1.00  0.00           H
END

An example tleap.in input:

# Load the TIP3P water model
source leaprc.water.tip3p

# Load the water molecules from the PDB file
m = loadpdb water5.pdb

# Create a periodic box (10×10×10 Å) around the system
solvatebox m TIP3PBOX 10.0

# Save the system to .prmtop and .inpcrd files
saveamberparm m water5.prmtop water5.inpcrd

# Exit LEaP
quit

An example minim.in input:

  Minimize 5-water cluster in periodic box
&cntrl
 imin=1,          ! Minimize
 maxcyc=500,
 ncyc=250,
 ntb=1,           ! Constant volume, periodic boundary
 cut=8.0,         ! Nonbonded cutoff
 ntpr=50,         ! Print every 50 steps
/

This prepares a geometry minimization of randomly placed TIP3P water molecules in a 10×10×10 ų cubic simulation box.

tleap -f tleap.in
sander -O -i minim.in -o minim.out -p water5.prmtop -c water5.inpcrd -r min.rst -ref water5.inpcrd

To avoid running AMBER on the head node, example job script for a regular AMBER SLURM job (subAMBER.sh) is provided:

#!/bin/bash
#SBATCH -J AMBER              # Job name
#SBATCH -t 24:00:00           # Max runtime
#SBATCH -p cpu               # Request CPU partition
#SBATCH -t 24:00:00           # Max runtime
#SBATCH -p cpu               # Request CPU partition
#SBATCH --ntasks=8            # Use 8 CPUs total

# Load AMBER module if needed (uncomment and adjust if applicable)
module purge
module load PrgEnv-gnu/8.3.3
module load gcc/12.2.0
module load cray-mpich/8.1.24
module load cray-libsci/23.09.1.1
module load amber/22

# Run Sander with 8 CPU
srun sander.MPI -O -i minim.in -o minim.out -p water5.prmtop -c water5.inpcrd -r min.rst -ref water5.inpcrd

To submit subAMBER.sh:

sbatch subAMBER.sh

AMBER for Converting Force Fields

To use Amber on Komondor, load the required module and activate the Amber environment:

module load amber
source /opt/software/packages/amber/22/amber.sh

This sets the environment variables so that Amber executables (e.g. tleap, antechamber) are available system-wide.

Amber includes a dedicated Python environment with installed modules such as parmed, pytraj, and others. To use Amber’s Python interpreter:

/opt/software/packages/amber/22/miniconda/bin/python

This environment ensures that ParmEd scripts work out of the box. To activate ParmEd in a Python script:

import parmed as pmd

Further information can be found in the ParmEd documentation and the Amber manual:

Citing Amber 2022

D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O’Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.

Last update by Milán SZŐRI: 2025-11-25