Amber Tools

What is Amber Tools?

AmberTools consists of several independently developed packages. The set can also be used to perform complete simulations of molecular dynamics, with explicit water or generalized models of birth solvent.

Overview

• NAB/sff: a program builds molecules, performs MD, or applies distance geometry constraints using generalized implicit solvent models of Born, Poisson-Boltzmann, or 3D-RISM
• Antechamber and MCPB: programs to create force fields for organic molecules in general and metal centers
• Tleap and parmed: basic preparation tools for amber simulations
• Sqm: semiempirical and quantum chemistry program DFTB
• PBSA: performs numerical solutions for Poisson-Boltzmann models
• 3D-RISM: solves integral equation models for solvency
• Sander: laboratory program for molecular dynamics simulations
• Mdgx: A program to expand the boundaries of Amber MD, mainly by adjusting parameters. It also includes customizable virtual sites and explicit MD solvent features.
• Cpptraj and pytraj: tools for structure and dynamic analysis in trajectories
• MMPBSA.py and amberlite: energy-based analyses of MD trajectories

Resources

• CUDA pbsa enabled
• Major updates to packmol memgen, a tool for building lipids and bilayers
• Rism3d: tree code analysis accelerations and support for periodic systems
• FEW: better paths to complex transformations; support for pmemd
• Sander: constant redox potential simulations; directional pressure escalation; QM/MM Interface for Fireball
• Moft: volumetric analysis of water/ion density using Lapatian analysis
• Continuous updates and extensions for cpptraj:
• Enhanced scripting skills
• More detailed changelog for cpptraj

• Constant md pH simulations
• Constant redox potential calculation to complement constant pH simulations

System Requirements

All Amber will compile and run on Ubuntu Linux platforms (and Debian variants like lubuntu, Kubuntu and xubuntu, and Windows 10 "subsystem for Linux").