Go to
VEGA Command Line

1. Introduction

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

3. Running VEGA ZZ

4. Mouse, keyboard and joystick

5. The main menu

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 a peptide
   6.14 Build a solvent cluster
   6.15 Build with SMILES
   6.16 Build IUPAC
   6.17 Save the molecule
   6.18 Merge with another file
   6.19 Save the trajectory
   6.20 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 ISIS/Draw 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

15. The HyperDrive Technology

16. Cluster rendering (WireGL)

17 Creating a new template
   17.1 Force field template
   17.2 Atomic charge template

18. Tutorials

19. How-to guide

20. Frequently Asked Questions (FAQ)

21. Compatibility list

22. Bugs

23. Development information
   23.1 Hardware for beta testing
   23.2 Development tools

24. History

25. Copyright and disclaimers

26. How to cite VEGA

27. Acknowledgements

  

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
   - VEGA On-line
   - VEGA SE
   - WakeUp
   - WarpBench
   - WarpGate
   - WarpKeyGen
   - WarpTel

Printable version