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¶
- HPC_AMBERTOOLS_DIR - installation directory
- HPC_AMBERTOOLS_BIN - executable directory
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