Last modified: July 23 2009 15:13:06.

Amber is a package of molecular simulations programs and associated molecular mechanics force fields used for the simulations of biomolecules. The current version is Amber 10.

The amber website, http://amber.scripps.edu, 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://amber.scripps.edu

Both serial and MPI versions exist for the sander program which does the actual molecular structure energy minimization.

• Version:Amber 10
• Machines:Arches cluster
• Location:
• Serial on all clusters (only use if running multiple single processor jobs at same time): /uufs/chpc.utah.edu/sys/pkg/amber/amber10/exe
• Generic parallel for single node runs on all clusters as well as multinode parallel on MM, TA, DA: /uufs/chpc.utah.edu/sys/pkg/amber/amber10/exe
• Sanddunearch multinode parallel: /uufs/sanddunearch.arches/sys/pkg/amber/amber10/exe
• Telluride multinode parallel: /uufs/telluride.arches/sys/pkg/amber/amber10/exe
• Updraft multinode parallel: /uufs/updraft.arches/sys/pkg/amber/amber10/exe
• Makena multinode parallel: /uufs/makena.arches/sys/pkg/amber/amber10/exe

To Use:

Use the interactive programs antechamber and xleap to help create the necessary input files.

	setenv AMBERHOME /uufs/chpc.utah.edu/sys/pkg/amber/amber10
	set path = ($path $AMBERHOME/exe)
	antechamber

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.

Below are links to several simple scripts that can be adapted to run sander to do a minimization of a structure.

• Single node run anywhere, multinode run on TA, DA, MM: rnamber_mpich2
• Multinode run on Sanddunearch: rnamber_sda
• Multinode run on Telluride: rnamber_telluride
• Multinode run on Updraft: rnamber_updraft
• Multinode run on Makena: rnamber_makena