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 10 is the latest version. Executables for it include pmemd, sander.MPI, and sander.LES.MPI (Locally Enhanced Sampling).

AMBER 9 is also installed on some platforms. Executables for it include pmemd, sander.MPI, sander.PIMD.MPI (Path-Integral Molecular Dynamics), and sander.LES.MPI (Locally Enhanced Sampling).

Installed on: pople, salk, and the Opteron cluster.

Pople version 10

Executables sander.MPI, sander.LES.MPI and pmemd reside in /usr/local/packages/AMBER10. Submit a batch job with commands to:

  1. Set up the module command
  2. Load the amber module 
    module load amber/10
  3. Run amber with a command similar to:

    mpirun -np x pmemd

    where x is the number of cores requested in the PBS directive -l nodes=y:ppn=x

AMBER9 is also installed. To use it, load the amber/9 module.

See a sample job.

Salk version 10

Executables sander.MPI, sander.LES.MPI and pmemd reside in /usr/local/packages/AMBER10. Submit a batch job with commands to run amber with a command similar to:

mpirun -np x /usr/local/packages/AMBER10/pmemd

where x is the number of cores requested in the PBS directive -l ncpus=x

See a sample job.

Opteron Cluster version 8.0

Executables reside in /usr/local/packages/Amber/amber8/exe. Submit a batch job containing a command similar to:

srun /usr/local/packages/Amber/amber8/exe/sander

Other AMBER documentation:

See also: