AMBER User Manual

Introduction.
- What to read next.
- Information flow in Amber.
- Preparatory programs.
- Energy programs.
- Analysis programs.
Installation of Amber 6
- Installing by hand.
- Installing on Win95/98/NT
- Testing.
- Memory Requirements.
The database directory.
An Amber Tutorial.
- Example 1. Minimization of BPTI in vacuum.
- Example 2. A more complicated protein example.
- Example 3: NMR refinement in explicit water solvent
- Example 4: Using a truncated octahedral box
LEaP
- Preface
- Introduction
- Concepts
- Starting LEaP
  - Verbosity
  - Log File
- Using LEaP
- teLEaP
- xLEaP
- Using LEaP With AMBER
- Commands
- Examples
Sander
- Introduction.
- History and credits
- Notes for users of earlier versions of Amber
- File usage.
- Example input files
- Overview of the information in the input file
- SECTION ONE: General minimization and dynamics parameters.
- SECTION TWO: Weight change information.
- SECTION THREE: File redirection commands.
- SECTION FOUR: Distance, angle and torsional restraints.
- SECTION FIVE: NOESY volume restraints.
- SECTION SIX: Chemical shift restraints.
- SECTION SEVEN: Direct dipolar couling restraints
- Overview of NMR refinement using SANDER.
LES
- Background.
- Preparing to use LES with AMBER
- Using the ADDLES program
- More information on the ADDLES commands and options
- Using the new topology/coordinate files with SANDER
- Case studies: Examples of application of LES
- Unresolved issues with LES in AMBER
- References for LES and other multiple-copy methods
CMC/MD
- Introduction to CMC/MD
- Input files
- OUTPUTS
Gibbs
- Introduction
- Free Energy Techniques Available in GIBBS
- Understanding the Output
- Defining States and Obtaining Appropriate Starting Coordinates
- Suggested introductory references
- Assigning files
- Control parameters
- Choices Affecting Free Energy Calculations
- References
Sander_classic
- Introduction.
- SECTION ONE: General minimization and dynamics parameters.
- SECTION TWO: Weight change information.
- SECTION THREE: File redirection commands.
- "SECTION
- SECTION FIVE: NOESY volume restraints.
- SECTION SIX: Chemical shift restraints.
ptraj
- ptraj command prerequisites
- ptraj input/output commands
- ptraj commands that modify the state
- ptraj action commands
- rdparm
- "rdparm
Carnal
- Contents
- Introduction
  - Input
  - Output
- Analin introduction
- Examples
- References
MM-PBSA
- General input variables
- Input variables for alanine/glycine scanning
- Sample input files
- The statistics program
- Auxiliary programs used by MM-PBSA
Profec
- Introduction
- makeGrid
  - makeGrid input format
- makeDiffGrid
- Field
- Data formats
- Examples
Nmode
- Introduction
- References
- General description
- Files
- Input description
- quasih
- Nmanal
- Lmanal
RESP
Miscellaneous
- Nucgen
- ambpdb
- protonate
- intense
- spectrum
- fantasian
- rdis
- curvop
Anal
- Introduction
- Files
- "Input
Appendices
- Appendix A: Namelist Input Syntax
- Appendix B: GROUP Specification
- Appendix C: Parameter Development
- Appendix D: Charge fitting philosophy
- Further Notes on Charge Derivation for the 1994 Force Field
Amber file formats
- parameter file format
- restart file format
- trajectory (coordinates or velocity) file format
Notes

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Updated on January 5, 2000. Comments to case@scripps.edu