Ambertools
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Description
AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the "regular" Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself.
Environment Modules
Run module spider ambertools to find out what environment modules are available for this application.
System Variables
- HPC_AMBERTOOLS_DIR - installation directory
Additional Information
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