ambertools¶
Description¶
AmberTools is a free, useful standalone package and a prerequisite for installing Amber itself. 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 libsander and libpbsa libraries use the LGPL license.
Environment Modules¶
Run module spider ambertools to find out what environment modules are available for this application.
Environment Variables¶
Additional Usage Information¶
AmberTools23 (released on April 28, 2023) consists of the following major codes:
| Tool | Function |
|---|---|
| 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 |
Categories¶
chemistry, molecular_dynamics