QUANTA Generating and Displaying Molecules is designed primarily for first-time users. You can read it to understand how to create, import, and edit molecules 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 since previous versions of QUANTA.
This book contains information for building, importing, editing, and manipulating 2D and 3D molecules. Performing these functions, using a variety of sketchers and builders, is described in Chapters 1, 2, 4, and 5.
Chapter 3 describes CHARMm, the calculation engine of QUANTA, and the processes for performing molecular energy and minimization calculations using CHARMm. Chapter 10 describes how to connect to other external applications for additional calculations and functions.
Chapters 6 and 7 describe ways to use graphical objects and various molecular representations to display and study structures.
Chapter 8 describes importing and exporting files to and from non-QUANTA programs. It includes the steps you take to make sure that any imported molecule is accurately represented within QUANTA.
Chapter 9 describes connecting to specific external calculation applications.
Information provided in progressive chapters is based on the assumption that you are familiar with basic software operations and with material in previous chapters.
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 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 and analysis.
Within each book, exercises are step-by-step procedures that may be linked across chapters. Datafiles may be 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 sequential 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:
In addition to the 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 Setting the QUANTA Environment and Starting QUANTA on pages 4-6 in the book QUANTA Basic Operations.
For this and subsequent startups, enter the command:
> cd ~/subdirectory
> quanta
QUANTA opens displaying the structure you worked on most recently in this directory. The Molecule Management table displays the structure's name and status.
Typographical conventions used in this book are:
Examples of file contents, information in the textport or on the message line |
|