Who should read this book
   What this book contains
   How to use the QUANTA introductory documentation set
   Documentation set roadmap
   Related documentation
   Restarting QUANTA
   Conventions

1. Sketching 2D Molecules

   Starting ChemNote
   Understanding the ChemNote window
      Menu bar
      Palette
      Message line
   Creating a 2D sketch
      Rings
      Bonds
   Changing atoms within a structure
      Carbon substitution
      Hydrogen atoms
   Customizing bonds
   Saving ChemNote structures
   Returning to Molecular Modeling
   Importing a .molfile into Molecular Modeling
   Using templates
      The Template window
      Title bar
      Menu bar
      Buttons
      Building a template-based structure
   Summary

2. Editing 3D Structures

   Creating a base structure
   Editing bonds and fragments
   Customizing the Fragment Table
   Altering atoms
   Minimizing a structure
   Saving a structure
   Saving and exiting with multiple structures
   Other editing options
   Summary

3. Calculating and Minimizing Energy

   Understanding basic CHARMm operations
      The CHARMm energy functions
      CHARMm theory
      CHARMm calculations
      QUANTA interaction with CHARMm
   Generating a potential energy value
   Performing a minimization
      Performing repeated minimizations
      Saving or rejecting calculation results
   The Merck Molecular Force Field
   Summary
   References

4. Building with Sequence Builder

   Understanding the Sequence Builder window
   Starting Sequence Builder
   Building a sequence
   Creating a peptide
   Minimizing a peptide
   Creating a cyclic peptide
   Summary

5. Using Other Build Applications

   Using Crystal Modeling
      Defining and incorporating symmetry information
      Using the Crystal Modeling palette
      Calculating CHARMm energy using images
      Modifying the asymmetric unit
   Using protein applications
   Using X-Ray applications
   Using NMR Structure Determination
   Summary

6. Using Graphical Objects

   Generating ribbons
   Generating a grid contour mesh
   3D vector displays
   QUANTA plot files
   Color scale
   Managing objects
   Solvent surfaces
   Displaying probe interaction results
   Displaying molecule interaction results
      Calculating electrostatic interactions only
   Managing maps
   Generating an electrostatic potential energy surface
      Calculating and displaying an electrostatic potential grid map
      Calculating and displaying an electrostatic potential dot surface
      Calculating and displaying an isoenergy 2D contour plots
   Generating an electrostatic field
   Generating and displaying hydrogen bonds
      Applying settings to other structures
   Summary
   References

7. Generating Visual Representations

   Rendering solid models
      Manipulating solid models
   Using the Solid Model window
   Sample procedure - Generating a solid model
      Generating cartoons of proteins and nucleic acids
   Generating solid surfaces
   Generating raytrace van der Waals models
   Generating display-only raster models
   Plots for hardcopy output
   MolScript plots
   Summary

8. Importing and Exporting Files

   Importing PDB files
      PDB import/export preferences
      PDB files containing multiple models
      Importing Protein Data Bank files
      Importing multiple PDB files
   Cleaning imported structures
      Splitting tools
      Cleaning tools
   Exporting an MSF

9. Using External Applications

   Accessing external programs from QUANTA
      Specifying a host
      Performing a calculation on a remote host
   Using CINDO
   Using MOPAC
   Executing a single-energy AM1 calculation
      Comparing MOPAC data
   Using UHBD
   Summary
      CINDO
      MOPAC
      UHBD
   References

© 2006 Accelrys Software Inc.