Comments Off on Amber


Amber is a suite of biomolecular simulation programs. The term “Amber” refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.

Set up the environment and version

ml simulation/amber

Available versions :

  • Amber 22
  • AmberTools 23


Running an amber command

$ ml simulation/amber
$ pdb4amber --version
usage: pdb4amber [-h] [-i FILE] [-o FILE] [-y] [-d] [-s STRIP_ATOM_MASK]
                 [-m MUTATION_STRING] [-p] [-a] [--constantph]
                 [--most-populous] [--keep-altlocs] [--reduce]
                 [--no-reduce-db] [--pdbid] [--add-missing-atoms]
                 [--model MODEL] [-l FILE] [-v] [--leap-template]
                 [--no-conect] [--noter]