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AmberTools17 is now available!

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license.

Option 1: Getting source code

This is the traditional way AmberTools has been distributed. It is recommended for most users, and is the requried path if you also want to get Amber. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.

The Reference Manual is available in pdf format, and included in the distribution. It may help you to see if AmberTools meets your needs.

Download AmberTools source code.

Option 2: Binary distribution via conda.

This is a new option: Users of the conda python system can install a serial, binary (pre-compiled) distribution as follows:

  conda install ambertools=17 -c http://ambermd.org/downloads/ambertools/conda/

This should work for Linux and MacOS systems, with python versions 2.7 to 3.6; but it is experimental, and does not provide access to parallel or gpu-optimized codes. This provides a simple way to get started with AmberTools, and to install it into many workflows, but it is not a substitute for the full source-code distributions listed above.

Option 3: Binary distribution without conda.

Non-conda users can follow:

  wget http://ambermd.org/downloads/install_ambertools.sh 
  # Or: curl http://ambermd.org/downloads/install_ambertools.sh -O 
  bash install_ambertools.sh -v 3 --prefix $HOME --non-conda 

To see more options:

  bash install_ambertools.sh -h 

The caveats listed above for Option 2 are relevent here as well.


Overview of AmberTools17

AmberTools17 (released on April 17, 2017) consists of the following major codes:

  • NAB: a program build molecules, run MD or apply distance geometry restraints using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
  • antechamber and MCPB: programs to create force fields for general organic molecules and metal centers
  • tleap and parmed: basic preparatory tools for Amber simulations
  • sqm: semiempirical and DFTB quantum chemistry program
  • pbsa: performs numerical solutions to Poisson-Boltzmann models
  • 3D-RISM: solves integral equation models for solvation
  • sander: workhorse program for molecular dynamics simulations
  • mdgx: a program for pushing the boundaries of Amber MD, primarily through parameter fitting. Also includes customizable virtual sites and explicit solvent MD capabilities.
  • cpptraj and pytraj: tools for analyzing structure and dynamics in trajectories
  • MMPBSA.py and amberlite: energy-based analyses of MD trajectories

Among the new features:

  • Force field updates:
    • Lipid17 force field for lipids<\li>
    • fb15 "force-balance" force field for proteins
    • OPC3: new rigid 3-point water model
    • Updates to the mdgx force-field development pipeline
  • CUDA-enabled

    pbsa

    solver; extensions for membrane modeling with PB
  • DFTB3 support in

    sqm

  • Major updates to the

    FEW

    free-energy workflow scheme
  • Extensions of the

    pytraj

    interface to trajectory analysis
  • Continued updates and extensions to cpptraj:
    • CUDA acceleration: for the closest and watershell commands
    • comparetop command for reporting differences between topologies
    • wavelet analysis via

      WAFEX

      (wavelet analysis feature extraction)
    • Speed improvements in

      SPAM

      , volmap and

      GIST

      analyses
  • More detailed changelog for

    cpptraj

"Insert clever motto here."

Last modified: Feb 10, 2018