AmberTools consists of several independently developed packages that work well by themselves, and with Amber24. 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 AmberTools24
AmberTools24 (released on April 30, 2024) consists of the following majorcodes:
- 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, andab initio quantum chemistry codes, for stand-alone calculations or inQM/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 forcefields
- 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
- FEW: Free energy workbench, with tools for varioustypes of free energy analyses
- fe-toolkit: routines to analyze alchemical free energy simulations
Among the new features (more coming soon):
- New and updated forcefields:
- Inclusion of the ABCG2 charge model for GAFF2
- Quick package for Hartree-Fock and DFT electronic stucture calculations, with GPU support. Quick is integrated into sander for QM/MM simulations, and AmberTools24 containssignificant performance improvements, support for f basis functions, an updated geometry optimizer, and supportfor spin-unrestricted calculations.
- cpptraj updates: (See also a Detailed changelog for cpptraj.)
- Fixed unwrapping and diffusion imaging for NPT trajectories.
- Added the ability to remove box fluctuations when unwrapping NPTtrajectories (by projecting on the average unit cell).
- Added an MPI-parallelized diffusion calculation from multiple timeorigins, as well as the toroidal-view preserving diffusioncalculation.
- For nucleic acid structure analysis, added the ability to writeaxes, take user specified base pairs, and report all hydrogen bonds(not just WCF).
- Added the ability to calculate total energy using OpenMM from theenergy command (if linked to OpenMM libraries).
- Added the ability to change the mass and/or charge of selected atoms.
- Added the ability to calculate the extended similarity score forstructures in a trajectory (J. Comp.-Aid. Mol. Design, 2022, 36,157-173).
- Added the ability to utilize and manipulate internal coordinates (Z-matrices).
- Added MPI parallelism and rotatable grids to GIST.
- Added the 'mergeres' keyword to 'change' command for mergingconsecutive residues.
- Added the ability to change mapped atom names in the 'atommap'command to reference names.
- Added the 'getbox' keyword to the 'box' command to allow extractingunit cell, fractional cell, or symmetric shape matrix data.
- Added the '--charge' command line flag for calculating charge andprinting to stdout.
- fe-toolkit updated package of routines to analyzealchemical free energy calculations.
