Go to
VEGA Command Line
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 Add fragments
6.8 Add hydrogens
6.9 Add a solvent cluster
6.10 Add ions
6.11 Remove dialogs
6.12 Build a solvent cluster
6.13 Save the molecule
6.14 Merge with another file
6.15 Save the trajectory
6.16 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 Mopac
8.4 Surface
8.5 Trajectory analysis
8.6 Molecular similarity
8.7 Selection tool
8.8 BioDock
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
10.4 Setting default parameters (prefs
file)
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 ClustalX plug-in
12.3 Dhrystone plug-in
12.4 Escher NG plug-in
12.5 Predator plug-in
12.6 PropKa plug-in
12.7 PowerNet plug-in
12.8 RamaPlot plug-in
12.9 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 OpenGL 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
19. Frequently Asked Questions (FAQ)
22. Development
information
22.1
Hardware for beta testing
22.2
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
- Interchange File Format
- PDB Fat
- PDB ATDL
- Raw Surface
- VEGA Selection
APPENDIX E Language
localization
- Introduction
- What you need
- How to make a new VEGA.catalog
- Notes
APPENDIX F
- Dielectric constants
BONUS SOFTWARE
- AMMP
- ESCHER NG
- Mopac 7.01-4
- WarpBench
- WarpGate
- WarpKeyGen
- WarpTel