amber
Software Description
AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs)- and a package of molecular simulation programs which includes source code and demos.
Info
Module Name
amber
Last Updated On
08/29/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
Software Description
AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs)- and a package of molecular simulation programs which includes source code and demos.
General Linux
To run this software interactively in a Linux environment run the command:
module avail amber
and choose the most recent version of the software applicable to your research. The exact name of the module will vary from machine to machine, and over time with new updates so be sure to study the list printed with the 'module avail' command demonstrated above. For example,
module load amber/11
The amber module requires and will automatically load several other modules. Pay attention to any error messages or warnings that result from loading the module as conflicts with other packages already loaded in your environment are a common source of error. An example submission script is below. Note that the #PBS lines need to be tuned for each cluster's policies. You may not need to run short jobs through the queue, so the program can be used interactively by loading the module and running the executable directly at the command prompt.
#!/bin/bash -l
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8
#PBS -m abe
module load amber
cd $PBS_O_WORKDIR
mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
AMP2md39.mdcrd
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