AMBER

Software Summary

Mesabi

Default Module:

14-cuda

Other Modules Available:

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

Last Updated On:

Wednesday, June 12, 2024

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

20-quick

Other Modules Available:

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

Last Updated On:

Wednesday, June 12, 2024

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Wednesday, June 12, 2024

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

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.

Software Documentation

Software Documentation Tabs

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 #PBS lines need to be tuned for each cluster's policies. 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 -l 
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8 
#PBS -m abe 

module load amber 

cd $PBS_O_WORKDIR 

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

AMBER

Mesabi

Mesabi K40

Mangi

Mangi v100

NICE

Software Documentation Tabs

Additional Documentation