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