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VEGA ZZ

1. Introduction

2. Installation
   2.1 Unix installation
       2.1.1 Building the VEGA package
       2.1.2 Setting-up your Unix system
   2.2 Windows installation
   2.3 AmigaDOS installation
   2.4 Printable manual

3. Usage
   3.1 INPUT…
   3.2 –a[RES_NUM]
   3.3 –b
   3.4 –c[TEMPLATE]
   3.5 –d[DIELECTRIC]
   3.6 –e[MOLECULE]
   3.7 –f[OUTPUT_FORMAT]
       3.7.1 Calculation formats
          3.7.1.1 Evaluation of interaction energy
          3.7.1.2 Information about the molecule
       3.7.2 Molecule formats
       3.7.3 Plot formats
       3.7.4 Surface formats
       3.7.5 VRML formats
   3.8 –g[RADIUS]
   3.9 –i[SHELL RAD SHAPE]
   3.10 –k[KEYWORDS]
   3.11 -l[MOLTYPE]
   3.12 –m[KEYWORDS]
   3.13 –n
   3.14 –o[OUTPUT]
   3.15 –p[FORCE_FIELD]
   3.16 -q[METHOD]
   3.17 –r
   3.18 –s[POINTS]
   3.19 -t[SECSTRUCT]
   3.20 -u
   3.21 –w

4. Examples

5. Default settings

APPENDIX A - Parameters
   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
   - InpMerge
   - Top2tem

Printable version