AMBER 6 MANUALS

All material is copyrighted. Unless noted otherwise in the text, the copyright is:

    All contents Copyright (c) 1986, 1991, 1995, 1997, 2000 University of California.
                             All Rights Reserved.

The manuals are presented in two formats: Acrobat (PDF) and html ('Main manual' only). The PDF version provides book-style formatting, and includes a few additional volumes. The html version of the Main manual is divided by program and downloads much faster than the PDF. Further, the html version is up-to-date, the PDF may only be generated at release time.

Updates to the Amber6 Manuals as they appear on the CD-ROM distribution.

Acrobat (pdf) format

This is updated less frequently.

Main manual
Interface for Amber a scripting language
Interface The scripting program
Roar new dynamics program (5.0)

Html version of 'Main manual'

Introduction
Installation
Database
Tutorial
Leap (Molecule setup)
Sander (Energy minimization, dynamics)
LES (Locally Enhanced Sampling)
CMC/MD (Chemical Monte Carlo/Molecular Dynamics)
Gibbs (Free energy)
Sander_classic
Ptraj (Trajectory analysis)
Carnal (Trajectory analysis)
MM/PBSA (Molecular mechanics- Poisson Bolzmann Surface Area)
PROFEC (Free energy grid)
Nmode (Normal modes)
Resp (Charge fitting) (nmode.txt)
Miscellaneous utilities Nucgen, Protonate, Intense, Spectrum, Fantasian, Rdis, Curvop
Appendices Namelist format, Group input, Parameter development, Charge fitting philosophy
File formats
Notes

Web Masters <webadmin@www.amber.ucsf.edu>

Last modified: Tue Jan 4 01:54:38 PST 2000