QUANTA Simulation, Search, and Analysis is designed primarily for first-time users. If you are in this category, read it to understand how to simulate molecular motion, search molecular conformations, and analyze the data generated from these procedures within QUANTA.
If you are an experienced user, read this book to review information on functionality and procedures for executing building and editing tasks of QUANTA or to update yourself on changes in QUANTA.
This book contains information on simulating motion in a molecular system, applying molecular constraints during CHARMm calculations, generating sets of molecular conformations, evaluating similarities among molecules, and analyzing data from these operations. Information provided in progressive chapters is based on the assumption that you are familiar with basic software operations and with material in previous chapters and in the other volumes in the QUANTA introductory documentation set.
Since this book is designed primarily for new users, neither the descriptions nor the tutorial exercises comprehensively document all aspects of using QUANTA.
The book is written assuming that you are familiar with:
Assumptions also are made that you have a home directory where you can create subdirectories, and a licensed copy of QUANTA installed on your workstation.
This book is part of a documentation set that introduces users to QUANTA. The set consists of:
Although each book is self-contained, information within the set flows in a logical sequence. You must be familiar with basic operations to successfully complete building and editing tasks; molecule preparation in the building and editing phase must precede simulation, search, band analysis.
Within each book, exercises are step-by-step procedures that may be linked across chapters. Data files are frequently modified or reused by several exercises.
Because of the sequential nature of the documentation set and of the exercises in each book, you will get the most coherent and complete view of the software if you go through the books in the proper order.
The table below lists key topics and where to find information about them in the introductory set of QUANTA books. Book names are abbreviated:
Each book contains a master index covering topics in all three books. Since aspects of a topic may be covered in a number of places, use the index as an important resource for locating all the information on a topic.
In addition to the QUANTA introductory books, other books in the QUANTA documentation set include:
Other QUANTA-related documentation is included with specific software application packages. This documentation includes:
This book assumes you have already run QUANTA. If you have not, refer to the configuration and start-up instructions in QUANTA Basic Operations.
For this and subsequent start-ups, enter the command:
> cd ~/subdirectory
> quanta
QUANTA opens, displaying the structure you have worked on most recently in the current directory. The Molecule Management Table displays the structure's name and status.
Typographical conventions used in this book are shown below:
Commands you type, dialog box choices, information in the Textport or on the Message line |
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