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 9.0 is the latest version. Executables for it include pmemd, sander.MPI, sander.PIMD.MPI (Path-Integral Molecular Dynamics), and sander.LES.MPI (Locally Enhanced Sampling).

Installed on: pople, Big Ben, 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.

Big Ben version 9.0

Executables sander and pmemd reside in /usr/local/packages/AMBER/amber9/exe. Submit a batch job with the qsub command which includes a line similar to:

pbsyod /usr/local/packages/AMBER/amber9/exe/pmemd

Bioinformatics and Codon 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:

• AMBER Home Page (Scripps) which includes links to tutorials, and Amber documentation.


• For further information please contact AMBER correspondence.

See also:

• Review the other Computational Chemistry packages installed on PSC systems.