AMBER 7.0

AMBER (Assisted Model Building with Energy Refinement) is the collective name for a suite of programs designed to carry out molecular dynamics simulations, particularly on biomolecules.

AMBER 7.0 represents a major change from the most recent previous version. Briefly, the major differences include: a completely updated force field for proteins and nucleic acids; faster algorithms for simulations with water; new algorithms and procedures for free energy simulations, including support for force fields with polarization terms; Ewald sum periodicity in the dynamics program Sander; faster and more powerful tools for NMR spectral simulations; a new program for fitting point electrostatic charges from quantum data; a new dynamics and free energy program.

• Setup
• Sander
• Running
• Components
• Examples
• Help

Setup

The modules package controls access to software.

To use AMBER 7.0, include the line:

module load amber

in your .profile or .login files, or type this command whenever you want to access AMBER for a single session. The command may also be included in a script which runs an AMBER job.

Sander

The program that most amber users will concentrate on is sander, which does molecular dynamics and energy minimizations. On bassi sander is a POE executable and may be be run in parallel like any other POE program.

Usage

Running AMBER

AMBER is run as a sequence of program modules. A typical calculation with AMBER follows the steps of structure creation, minimization, dynamics, and finally analysis. The following notes indicate the functionality of each module. See the tutorial for hands on examples.

Preparatory Programs

These modules assemble basic data, such as cartesian coordinates, topology and force field parameters, for the energy and dynamics programs.

LEaP

is the primary program to create a new system in Amber, or to modify old systems. It combines the functionality of prep, link, edit, and parm from earlier versions.

PROTONATE

This program will add hydrogens in appropriate locations to peptides and proteins that lack them. It can also check the suitability of protons that are already present, and convert from one naming system to another (e.g. from IUPAC-IUB recommendations to Brookhaven format.)

Energy Programs

These are the actual simulation and minimization programs.

SANDER

is the basic energy minimizer and molecular dynamics program. This program relaxes the structure by iteratively moving the atoms down the energy gradient until a sufficiently low average gradient is obtained. The molecular dynamics portion generates configurations of the system by integrating Newtonian equations of motion.

GIBBS

is the free energy perturbation program. It is similar to SANDER, but uses the ensemble of generated configurations to calculate the free energy difference between two similar states.

NMODE

is both an energy minimizer and vibrational analysis program. NMODE can calculate the normal modes of the system as well as numerous thermochemical properties.

ROAR

is a "Penn State" version of sander, that incorporates a variety of features not found in sander itself. The most notable change is the incorporation of the ability to define a part of the system quantum-mechanically, allowing it to interact with other parts of the system that are defined in a molecular mechanics sense.

Analysis Programs

These modules interpret the results generated by AMBER.

CARNAL

is a molecular dynamics analysis program. It is used for geometrical measurements, root mean square coordinate fitting, trajectory averaging, and other structural analyses of MD trajectories.

PTRAJ

is a general purpose utility that can examine and modify prmtop files created by LEaP or PARM. It can also process trajectory files created from MD simulations, carrying out superpositions, extractions of coordinates, etc.

NMANAL/LMANAL

computes atomic fluctuations and various correlation functions from normal modes.

MM-PBSA

is a script that automates energy analysis of snapshots from a molecular dynamics simulation using ideas generated from continuum solvent models.

Examples

• Energy Minimization: BPTI (536 atoms)
• Long running simulations: JobSteps

Help

The AMBER documentation directory $AMBERHOME/doc contains complete documentation and an introductory tutorial in Chapter 4, which is useful for getting started.

The AMBER Home Page contains an up-to-date resource for tutorials, documentation, and discussion groups.