Amber Usage

Amber is a package of molecular simulations programs and associated molecular mechanics force fields used for the simulations of biomolecules. The current version is Amber20 built with the new AmberTools20 .

The amber website, http://ambermd.org, includes program descriptions, manuals, FAQ, as well as tutorials to get started with amber. In addition there is an Amber Mail Reflector that you can subscribe to that is a useful forum for the discussion of the use of the software.

Beginning users are strongly encouraged to go through the AMBER tutorials that come with each distribution. They can also be easily accessed at http://ambermd.org/tutorials

There is now a single build that runs on all clusters.  Both serial and MPI versions exist for the cpptraj, mdgx, MMPBSA.py,sander, sander.LES, pmemd and pmemd.amoeba programs; cuda versions also exist for pmemd and cpptraj.

• Version: Amber20
• Machine: all clusters
• Location: location determined by the Spack package manager

To Use:

For the latest version

module load gcc/8.5.0  intel-oneapi-mpi/2021.4.0 amber/20.20
or for the GPU version
module load gcc/8.5.0  intel-oneapi-mpi/2021.4.0 amber/20.20-gpu

 If using antchamber you can then

antechamber 

To get listing of usage options use: antechamber -h

If using xleap:

xleap

For xleap: once started using the command xleap, entering 'help' gives all commands and 'help <command>' gives a description of the usage of that command. Note that you must make sure that NumLock is not on for the pulldown menus in xleap to properly work.

A sample script that can be adapted to run amber:  /uufs/chpc.utah.edu/sys/installdir/amber/etc/rnamber20.slurm 

For help  please contact CHPC at helpdesk@chpc.utah.edu.