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 a 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 is provided:
#!/bin/bash
#SBATCH -J AMBER # Job name
#SBATCH -t 00:10:00 # Max runtime: 10 minutes
#SBATCH -p cpu # Request CPU partition
#SBATCH --ntasks=8 # Use 8 CPUs total
# Load AMBER module if needed (uncomment and adjust if applicable)
module load amber/22
# Run Sander with 8 CPUs
mpirun -np 8 sander.MPI -O -i minim.in -o minim.out -p water5.prmtop -c water5.inpcrd -r min.rst -ref water5.inpcrd
Last update by Milán SZŐRI: 2025-05-12