AMBER 6 Manuals - Sander_classic

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

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

• Introduction.
• SECTION ONE: General minimization and dynamics parameters.
  • General flags describing the calculation.
  • Nature and format of the input.
  • Nature and format of the output.
  • Potential function.
  • The soft repulsion option.
  • Polarizable potentials.
  • Frozen or restrained atoms.
  • Energy minimization.
  • Molecular dynamics.
  • Temperature regulation.
  • PEACS temperature algorithm
  • Pressure regulation
  • SHAKE bond length constraints.
  • Special water treatment.
  • Water cap.
  • NMR refinement options.
  • Particle Mesh Ewald.

• SECTION TWO: Weight change information.
• SECTION THREE: File redirection commands.
• "SECTION
• SECTION FIVE: NOESY volume restraints.
• SECTION SIX: Chemical shift restraints.