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AMBER

Introduction

The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs. It can perform molecular mechanics-Poisson Boltzmann/surface area, chemical Monte Carlo/molecular dynamics, protein structure refinement by locally enhanced sampling methodology, NMR refinement, and enzymatic mechanism modeling. It performs well as black-box software for structure-based ligand design. The AMBER Home Page has additional information.

Version

The versions currently available at OSC are 7.0, 8.0 and 9.0.

Availability

AMBER is available on the IBM Opteron Cluster, the Intel P4 Cluster, the BALE Cluster and the HP Itanium-2 Linux Cluster.

Usage

Users must complete a license agreement.

AMBER Usage on the Clusters at OSC

Location

The root of the AMBER directory tree is /usr/local/amber/.

Execution

AMBER usage is controlled via modules. Load one of the AMBER modulefiles at the command line, in your shell initialization script, or in your batch scripts, for example:

module load amber

Examples

Input files for the examples in the manual are in the examples subdirectory. Other examples can be found in the test and benchmarks subdirectories.

Input files for some of the web tutorials are in the tutorial subdirectory.

Documentation

General documentation is available from the AMBER Home page and in the local machine directories.