Amber

Overview

AMBER (Assisted Model Building with Energy Refinement) is a general purpose molecular mechanics/dynamics suite which uses analytic potential energy functions,derived from experimental and ab initio data, to refine macromolecular conformations.

AMBER version 7.0 is available on the Origin and Altix machines.

AMBER version 8.0 has been ordered for the CSAR machines and will be placed on the system at the earliest opportunity. For a benchmark comparison of the improved speed of Amber 8 on an IBM SP2 machine see their benchmark page.

Restrictions on Use

There are no restrictions on the use of the executable software for most CSAR users, however you will need to contact a member of the CSAR frontline team in order to be added to the access control list for the code. Any users of the CSAR service from for-profit organisations must have a signed licence agreement with the University of California, San Francisco in order to use the Amber software.

Set Up Procedure

Once you have been added to the access control list you will be able to access Amber using the module command. There may be several versions of Amber on the system at any one time, each of which will have its own module. To see which versions are available type module avail, and then load the appropriate module, for example module load amber7.

Running the Code

The versions of Amber on the CSAR Origin systems which are loaded using modules containing the string _mpi are MPI codes and should therefore be launched using the mpirun command. For example to run the sander code with 16 processors you would add the following to your batch script (where ... represent any additional arguments you would pass to sander)

The versions of Amber on the CSAR Origin systems which are loaded using modules containing the string _smp are OpenMP codes and should therefore be launched as if they were serial codes after setting the OMP_NUM_THREADS environment variable. For example to run the sander code with 16 processors you would add the following to your batch script (where ... represent any additional arguments you would pass to sander)

The versions of Amber on the CSAR Altix system are MPI codes and should therefore be launched using the mpirun command. For example to run the sander code with 16 processors you would set the number of processors to 16 in the options to the bsub command and then add the following to your batch script (where ... represent any additional arguments you would pass to sander)

mpirun -np 16 sander ...

Refer to the Amber manuals for further information on running the codes.

Further Information

AMBER is fully described in the following manuals (pdf format):

• Amber 7
• Amber 8
• The Amber web sites