LEaP

Preface

is the generic name given to the programs and , which are generally run via the tleap and xleap shell scripts. These two programs share a common command language but the program has been enhanced through the addition of an X-windows graphical interface. The name is an acronym constructed from the names of the AMBER software modules it replaces: prep, link, edit, and parm. Thus, can be used to prepare input for the AMBER molecular mechanics programs. However, the utility of is not limited to this task.

The User's Manual is intended to provide a comprehensive description of the programs and from a user's perspective. After reading the manual, the user ought to be able to run either the or program to obtain meaningful results. Also, the user should be able to understand the methods used by during the process of constructing molecules and generating input for other computational chemistry programs.

There are very few prerequisites for understanding or this manual. We have tried to write the manual so a person with a minimal background in chemistry and/or computers can understand the material. The material is frequently presented in more than one format to aid in comprehension.

It was our goal to write a user manual that provided a thorough and comprehensive presentation of the program. The information in this manual includes:

· examination of the concepts involved in running

· the use of in creating input for the AMBER and SPASMS programs

· discussion and comparison of the terminal and X-windows versions

· explanation of all chemistry-related algorithms used in

· descriptions and examples of each command

· several practical examples of running to build specific molecules.

Researchers using should use the following citation when referencing the program: Christian E. A. F. Schafmeister, Wilson S. Ross and Vladimir Romanovski, , University of California, San Francisco (1995). was developed in Peter A. Kollman's laboratory at the University of California-San Francisco. Its development was supported, in part, by the Defense Advanced Research Projects Agency under contract N00014-86-K-0757 administered by the Office of Naval Research (Robert Langridge, PI.). The software and documentation are provided to users pursuant to a license agreement containing restrictions on its disclosure, duplication, and use.

We gratefully acknowledge the Computer Graphics Laboratory (cgl: Robert Langridge, PI) for providing code that was used as the foundation for the pdb routines in . Financial support from the Defense Advanced Research Projects Agency under contract N00014-86-K-0757 administered by the Office of Naval Research (Robert Langridge, PI.) is appreciated. We wish to thank W. L. Jorgensen for providing the Monte Carlo equilibrated box of TIP3P water which is included in the distribution.