AmberTools23 is now available!

AmberTools consists of several independently developed packages that work well by themselves, and with Amber22. 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 has the LGPL license.

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Overview of AmberTools23

AmberTools23 (released on April 28, 2023) consists of the following major codes:

nabc/sff: tools to build molecules, run MD or apply restraints using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models

antechamber and MCPB.py: programs to create force fields for general organic molecules and metal centers

tleap and parmed: basic preparatory tools for Amber simulations

sqm and Quick: semiempirical, DFTB, and ab initio quantum chemistry codes, for stand-alone calculations or in QM/MM

pbsa: performs numerical solutions to Poisson-Boltzmann models

3D-RISM: solves integral equation models for solvation

sander: workhorse program for molecular dynamics simulations

gem.pmemd: tools for using advanced force fields

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: energy-based analyses of MD trajectories

fe-toolkit: routines to analyze alchemical free energy simulations

Among the new features:

New and updated forcefields:

OL21 update for DNA
Update to GAFF2, version 2.20
Updated parameters for some post-translational modifications

Quick package for Hartree-Fock and DFT electronic stucture calculations, with GPU support. Quick is integrated into sander for QM/MM simulations, and AmberTools23 contains significant performance improvements, a new geometry optimizer, and support for spin-unrestricted calculations.

Detailed changelog for cpptraj. Changes include GIST improvements, new cluster analysis, and a "prepareforleap" script with support for carbohydrates.

fe-toolkit package of routines to analyze alchemical free energy calculations.