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 11, 10 and 9 are installed on various platforms.
Executables for AMBER 10 include pmemd, sander.MPI, and sander.LES.MPI (Locally Enhanced Sampling).
Executables for AMBER 9 include pmemd, sander.MPI, sander.PIMD.MPI (Path-Integral Molecular Dynamics), and sander.LES.MPI (Locally Enhanced Sampling).
Installed on: blacklight, salk, and the Opteron cluster.
Blacklight version 11
Executables reside in /usr/local/packages/AMBER11/.
- Prepare a batch job containing commands to:
- Set up the module command
- Load the amber module
module load amber
- Run AMBER with a command like:
mpirun -np x pmemd.MPI -arguments
where x is the number of cores requested in the PBS directive -l ncpus=x
- Submit the job with the qsub command.
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. The command to run MMPSA.py.MPI should be:
mpirun -np x 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.
- Prepare a batch job which:
- Executes 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
- Executes amber with a command similar to:
- Submit the job with the qsub command.
