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QUANTA 2006 Simulation, Search, and Analysis |
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. Executing CHARMm Dynamics
Commands in the CHARMm pulldown
Running CHARMm dynamics calculations
Heating
Equilibration
Simulation
Saving dynamics output
Executing dynamics animation
Sample procedure - Dynamics animation
Create an animation with an energy trace
Summary
References
2. Applying Constraints
Defining and applying atom constraints
Sample procedure - Defining and applying atom constraints
Defining and applying distance constraints
Defining and applying torsion constraints
Sample procedure - Defining and applying distance and torsion constraints
Applying stochastic boundary constraints
Summary
3. Defining Geometric Properties
Understanding Torsion Manipulations
Defining Torsion Angles
Interactively Defining Torsion Angles
Specifying Torsion Angles and Families
Saving and Restoring Torsion Angle Definitions
Selecting Torsions
Dealing with Cyclic Structures
Defining Other Geometric Properties
Sample Procedure - Defining Torsion Angles
Summary
4. Understanding Search Methods
Using a Systematic Search Method
Using a Stochastic Search Method
Performing a Conformational Search
Setting Up a Background Search
Performing a Search on More than One Structure
Using Tags
Understanding the Grid Scan Search
Understanding the Custom Search
Understanding Cyclic Modeling
Understanding Random Sampling Search
Understanding Random Minimization
Understanding the Boltzmann Jump Search
Choosing Boltzmann Jump Parameters
Understanding the Hybrid Jump Search
Understanding the Custom RIS Search
Understanding RIS Random Sampling
Understanding the Filter Search
Understanding the Peptide Flip Search
Understanding Loop Modeling
Additional Processing of Conformations
Summary
References
5. Performing a Search
Performing a Grid Scan Search
Sample Procedure - Grid Scan Search
Performing a Second Grid Scan Search
Performing a Random Sampling Search
Sample Procedure - Random Sampling Search
Performing a Boltzmann Jump Search
Sample Procedure - Boltzmann Jump Search
Performing a Search Using the Peptide Flip
Sample Procedure - Peptide Flip Search
Summary
6. Analyzing Results
Using the Analysis and Plots Palettes
Sample Procedure - Using the Analysis Palette
Sample Procedure - Using the Plots Palette
Additional Processing of Conformations
Using Overlay Structures
Sample Procedure - Using Overlay Structures
Creating 2D Plots and Making Selections
Using a Potential Energy Trace to Create a Subset of Conformations
Sample Procedure - Create a Conformation Subset
Creating a Range Map
Using Scatter Plots
Sample procedure - Scatter Plot
Using Correlation Maps
Sample Procedure - Generating a Correlation Map
Comparing Conformations
Sample Procedure - Comparing Structures from Two Files
Creating and Analyzing Clusters
Selecting Clusters
Sample Procedure - Generating and Analyzing a Cluster
Analyzing Trajectory Files
Sample Procedure - Analyzing a Trajectory File
Summary
7. Examining Molecular Similarity
Creating Structures
Sample Procedure - Building Molecules
Managing Structures
Sample Procedure - Atom Matching Preparation
Matching Atoms
Sample Procedure - Matching Atoms in Two Structures
Matching Atoms in Three or More Structures
Sample Procedure - Matching Atoms for Three or More Structures
Performing Structural Fitting
Sample Procedure - Fitting
Performing Volume Fitting
Sample Procedure - Volume Calculations
Using MSF Bundles for Multiple Conformers
Sample Procedure - Using MSF Bundles
Summary
8. Using Tables
Using Objects Specific to Tables
Operating Within the Table Window
Mouse Actions
Keyboard Actions
Using Table Menus
Summary
9. Generating Graphs
Using Objects Specific to Graph Plotting
Using Graph Plotting Menus
Summary