AMBER Archive (2002)

Subject: Release of Amber, version 7 (fwd)

From: amber mail account (amber_at_heimdal.compchem.ucsf.edu)
Date: Sun Mar 03 2002 - 17:13:26 CST

---------- Forwarded message ----------
Date: Fri, 1 Mar 2002 16:23:55 -0800 (PST)
From: David Case <case_at_scripps.edu>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Release of Amber, version 7

                 Amber 7 released March 1, 2002

It gives us great pleasure to announce the availability of Amber 7, a
software package that implements a variety of molecular simulation-based
research techniques. The key new features of this release are listed below.
We hope these inspire you to license it. Funds for licensing Amber 7 go to
support further research by authors of the program; by licensing the
program, you are supporting such research.

The academic price for licensing is the same as for Amber 6, $400. (This
fee may be reduced or waived in special circumstances.) The industrial
price is $20,000 for new licensees and $15,000 for those who have licensed
Amber 6.

To proceed with ordering Amber 7, please follow the instructions at:

                   http://www.amber.ucsf.edu/amber
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Amber is the collective name for a suite of programs that allow users to
carry out molecular dynamics simulations, particularly on biomolecules. None
of the individual programs carries this name, but the various parts
work reasonably well together, and provide a powerful framework for many
common calculations.

The term "Amber" is also sometimes used to refer to the empirical force
fields that are implemented in the code. It should be recognized however,
that the code and force field are separate: several other computer packages
have implemented the Amber force fields, and other force fields can be
implemented with the Amber programs. Further, the force fields are in the
public domain, whereas the codes are distributed under a license agreement.

Peter Kollman, who had inspired and led Amber development for more than two
decades, died unexpectedly in May 2001. But many of the items cited below
(particularly in force field development) were very near completion at the
time of his death, and represent the culmination of several years of effort
from both Peter and his collaborators. The Amber development team is
committed to continuing to update and improve the software and force fields,
and we dedicate Amber 7 to Peter's memory.

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Amber 7 (2002) represents a significant change from the current version,
Amber 6, which was released in December, 1999. Briefly, the major
differences include:

(1) Several new force fields are available for proteins and nucleic acids.
These include versions with polarizable dipoles on atoms, and off-center
charges (also called "extra points", and analogous to lone pairs). Amber
now provides direct support for TIP3P, TIP4P, TIP5P, SPC/E and POL3 models
of water, as well as providing models for chloroform and other organic
solvents.

(2) A new "general amber force field" that should be applicable to most
organic molecules. The automated code to prepare Amber input files using
this force field is a new module, called Antechamber. In most cases,
Antechamber can directly convert three-dimensional models into files
appropriate for molecular mechanics calculations, automatically assigning
atom types, charges and force field parameters.

(3) Implementation of three new variants of the generalized Born (GB) code,
including one that appears to provide a better energy balance between
surface-exposed and buried atoms.

(4) More efficient PME simulations, with better performance on both
single-processor and parallel machines.

(5) Updated scripts for MM_PBSA analysis, making input easier to create and
providing more options for analysis of the results.

(6) Free energy calculations using the thermodynamic integration method can
now be carried out in sander. Many investigations that used to require
gibbs can now be carried out in a simpler fashion, and free energy studies
using the GB model or "extra points" force fields (which are not supported
with gibbs) can now be undertaken.

(7) New types of restraint forces can be defined that are based on RMS
superpositions to reference structures. This "targeted MD" capability can
be used to enhance or guide conformational sampling.

AMBER authors:

David A. Case, David A. Pearlman, James W. Caldwell, Thomas E. Cheatham III,
Junmei Wang, Wilson S. Ross, Carlos Simmerling, Tom Darden, Kenneth M. Merz,
Robert V. Stanton, Ailan Cheng, James J. Vincent, Mike Crowley, Vickie Tsui,
Holger Gohlke, Randall Radmer, Yong Duan, Jed Pitera, Irina Massova, George
L. Seibel, U. Chandra Singh, Paul Weiner, and Peter A. Kollman