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VEGA Command Line
2. Installation & activation
2.1 Installation of optional components
2.1.1 OpenCL acceleration
2.1.2 Live CD creator
2.1.3 MOPAC 2016
2.1.4 NAMD
2.1.5 PLANTS
2.1.6 X-Score
2.2 Asus Eee PC installation
2.3 Printable manual
4. Mouse, keyboard and joystick
6. Editing
6.1 Atoms
6.2 Atom properties
6.3 Atom constraints
6.4 Centroids
6.5 Bonds
6.6 Angles and torsions
6.7 Secondary structure
6.8 Add fragments
6.9 Add hydrogens
6.10 Add a solvent cluster
6.11 Add ions
6.12 Remove dialogs
6.13 Build DNA/RNA
6.14 Build a peptide
6.15 Build a solvent cluster
6.16 Build SMILES
6.17 Build IUPAC
6.18 Save the molecule
6.19 Merge with another file
6.20 Save the trajectory
6.21 The clipboard
7. Display
7.1 Atom selection
7.2 Display modes
7.3 View settings
7.4 Molecule colors
7.5 Color settings
7.6 Light settings
7.7 Molecule information
7.8 Hydrogen bonds
7.9 Save the image
7.10 Video encoding
8. Calculations
8.1 Charges & pot.
8.2 Ammp
8.3 NAMD
8.4 Mopac
8.5 Surface
8.6 Trajectory analysis
8.7 Molecular similarity
8.8 Selection tool
8.9 Interactions
9. Databases:
9.1 Open/create
9.2 Database explorer
10. Settings:
10.1 HID configuration
10.2 Host configuration
10.3 Preference editor
11. Integrated Tools:
11.1 GraphEd
11.2 MiniEd
11.3 OpenGL Setup
11.4 SendVegaCmd
11.5 Task manager
11.6 Top2Tem
11.7 WinDD
12. Plug-in system
12.1 Introduction
12.2 ChemSol plug-in
12.3 ClustalX plug-in
12.4 Dhrystone plug-in
12.5 Escher NG plug-in
12.6 FAME plug-in
12.7 MassTools plug-in
12.8 MetaQSAR plug-in
12.9 OSRA plug-in
12.10 Pockets plug-in
12.11 PowerNet plug-in
12.12 WarpEngine Technology
12.13 Predator plug-in
12.14 PropKa plug-in
12.15 RamaPlot plug-in
12.16 Stride plug-in
12.17 Plug-in SDK
13. Script engines
13.1 C scripts
13.2 REBOL
13.3 Included scripts
14. Extended commands
14.1 Introduction
14.2 Standard commands
14.3 Accessing to databases
14.4 VEGA ZZ commands
14.5 Dialogs & GUI
14.6 Graphic commands
14.7 Fmod
16. Cluster rendering (WireGL)
17 Creating a new template
17.1 Force field template
17.2 Atomic charge template
20. Frequently Asked Questions (FAQ)
23. Development information
23.1 Hardware for beta testing
23.2 Development tools
APPENDIX A
Gasteiger-Marsili parameters
APPENDIX B
VEGA prefs file
APPENDIX C - Templates
- CVFF atom types
- TRIPOS atom types
- UNIV atom types
APPENDIX D - File formats
- CSV Surface
- Database formats
- Interchange File Format
- PDB Fat
- PDB ATDL
- Raw Surface
- Score XML
- VEGA Selection
APPENDIX E - Language localization
- Introduction
- What you need
- How to make a new VEGA.catalog
- Notes
APPENDIX F
- Dielectric constants
APPENDIX G
- Error codes
APPENDIX H - MySQL quick guide
- Server configuration
- Client configuration
- SQL basic commands
BONUS SOFTWARE
- AMMP
- ESCHER NG
- GriDock
- InpMerge
- Live CD Creator
- Mopac 7.01-4
- Scripts for the command prompt
- ShutDownGUI
- Tree2C
- WakeUp
- WarpBench