amber

Drug Discovery Structural Biology Molecular Modeling and Simulation

Software Description

AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs)- and a package of molecular simulation programs which includes source code and demos.


Info

Module Name

amber

Last Updated On

06/12/2024

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://ambermd.org

Documentation

General Linux

To run this software interactively in a Linux environment run the command:

module avail amber

and choose the most recent version of the software applicable to your research. The exact name of the module will vary from machine to machine, and over time with new updates so be sure to study the list printed with the 'module avail' command demonstrated above. For example,

module load amber/11

The amber module requires and will automatically load several other modules. Pay attention to any error messages or warnings that result from loading the module as conflicts with other packages already loaded in your environment are a common source of error. An example submission script is below. Note that the #SBATCH parameters should be adjusted based on your job requirements. You may not need to run short jobs through the queue, so the program can be used interactively by loading the module and running the executable directly at the command prompt.

#!/bin/bash
#SBATCH --nodes=2 --ntasks-per-node=8
#SBATCH --mem=16gb
#SBATCH --time=24:00:00
#SBATCH --mail-type=ALL

module load amber

cd $SLURM_SUBMIT_DIR

mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
  AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
  AMP2md39.mdcrd

Agate Modules

Default

20-quick

Other Modules

20, 20-quick, 14, 14-cuda, 14-intel