Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

AMBER

AMBER (Assisted Model Building and Energy Refinement) uses potentials developed by Peter Kollman's group. AMBER takes a list of macromolecular residues which it links using standard geometrical parameters. The user adjusts this skeleton and generates parameters for the force field. Then energy minimization, molecular dynamics, or free energy perturbation calculations may be made. Setting up systems for use of AMBER programs should be done on your local machine.

AMBER versions 12, 11 and 10 are installed on various platforms.

Executables for AMBER 11 and 12 include pmemd.MPI, sander.MPI, and sander.LES.MPI (Locally Enhanced Sampling).

Executables for AMBER 10 include pmemd, sander.MPI, and sander.LES.MPI (Locally Enhanced Sampling).

Installed on: blacklightsalk.

Blacklight usage

To run a job using AMBER, you  must:

  1. Prepare a batch job containing commands to:
    1. Set up the module command
    2. Load the correct amber module for the version you wish to run.

      See documentation on the module software to determine

      To load the default version, type

      module load amber
    3. Run AMBER with a command like:
      mpirun -np $PBS_NCPUS pmemd.MPI  -arguments

      $PBS_NCPUS is automatically set to the number of cores requested in the PBS directive -l ncpus. 

  2. Submit the job with the qsub command.

Please note: Some version 11 executables require additional modules and additional executables. For example, to use the MMPSA.py.MPI module, the python and mpi4py modules must also be loaded, and python must be called before AMBER. To run MMPSA.py.MPI use this sequence of commands:

module load amber
module load python
module load mpi4py
mpirun -np $PBS_NCPUS python2.7-mpi ${AMBER11}/exe/MMPPBSA.py.MPI -arguments

If you are having trouble using AMBER, please contact PSC User Services.

Salk version 10

Executables sander.MPI, sander.LES.MPI and pmemd reside in /usr/local/packages/AMBER10.

  1. Prepare a batch job which:
    1. Executes amber with a command similar to:
      mpirun -np $PBS_NCPUS /usr/local/packages/AMBER10/pmemd

      $PBS_NCPUS is automatically set to the number of cores requested in the PBS directive -l ncpus. 

  2. Submit the job with the qsub command.