Amber is a package of molecular simulations programs and associated molecular mechanics force fields used for the simulations of biomolecules. The current version is Amber14; Amber12 still exists and can be used by replacing references to amber14 below and in the attached scripts to amber12.
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
Different builds have been done for each cluster to take advantage of differences in the internode connections. The version for lonepeak is built with mpich2; the others with mvapich2. Both serial and MPI versions exist for the cpptraj, mdgx, MMPBSA.py, sander, sander.LES, pmemd and pmemd.amoeba programs.
- Version: Amber14
- Machine: ember, kingspeak, ash and lonepeak
- Ember: /uufs/ember.arches/sys/pkg/amber/amber14/bin
- Kingspeak: /uufs/kingspeak.peaks/sys/pkg/amber/amber14/bin
- Ash: /uufs/ash.peaks/sys/pkg/amber/amber14/bin
- Lonepeak: /uufs/chpc.utah.edu/sys/pkg/amber/amber14/bin
Use the interactive programs antechamber and xleap to help create the necessary input files. The example below is for ember; substitute the appropriate path for other clusters.
setenv AMBERHOME /uufs/ember.arches/sys/pkg/amber/amber14
set path = ($path $AMBERHOME/bin)
To get listing of usage options use: antechamber -h
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.
The ember, ash and kingspeak executables are built with mvapich2; the lonepeak executable with mpich2
Below are links to several simple scripts that can be adapted to run sander to do a minimization of a structure.