National University of Singapore

Amber (Assisted Model Building and Energy Refinement) is a software package for molecular dynamics simulations, particularly for proteins, nucleic acids and carbohydrates. It's also a family of force field for molecular dynamics of biomolecules. The Amber software package is distributed by UCSF subject to a licensing agreement.

AMBER 10 is installed in /app1/linux/amber10 (On Atlas4 Cluster)  and  /app1/linux/amber10b (On Atlas5 Cluster) directory. Executables for it include sander, sander.LES and MPI parallel version sander.MPI, and sander.LES.MPI. AMBER 9 is installed in /app1/linux/amber9 (For Atlas3 Cluster) directory. Executables include sander, sander.LES, sander.PIMD and the MPI parallel version sander.MPI, sander.PIMD.MPI , and sander.LES.MPI.

The MPI parallel Amber jobs can be submitted to the HPC systems through atlas3_parallel, atlas4_parallel and atlas5_parallel queues. The following shows you how to submit a Amber10 parallel sander jobs to the atlas5_parallel queue:

[atlas5-c01]$ bsub < run_amber10

Sample run_amber10 script file:

-----------
#!/bin/sh
#BSUB -o my_amber10_job.eo
#BSUB -q 8core_parallel
#BSUB -n 16  (note: 8 ? n ? 32 )
#BSUB -a mvapich

mpirun.lsf /app1/linux/amber10b/exe/sander.MPI -O -i test.in -p apo.prmtop -c apo.inpcrd -o test.out -r test.rst -ref apo.rst -x test.mdcrd -inf test.info
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All jobs should be submitted from relevant working directories on the particular cluster, e.g., submit jobs to atlas3_parallel from /atlas3tmp on the atlas3 cluster, submit jobs to atlas4_parallel from /atlas4tmp on the atlas4 cluster, submit jobs to atlas5_parallel from /atlas5tmp on the atlas5 cluster.

Various applications in Ambertools, including antechamber and LEaP ( tLEap and xLEap), and the analysis program ptraj is available from the MobileVisLab. Just issue these commands: anterhamber, tleap, xleap or ptraj at the command prompt to start the applications.

Please contact us should you have any queries.