APPENDIX B – VEGA prefs file

This is an example of VEGA prefs file. This file must be placed in Data directory.

;               ********************************************
;               ****       VEGA V1.1 - Preferences      ****
;               **** (c) 1997-2000, Alessandro Pedretti ****
;               ****         All rights reserved        ****
;               ********************************************

; This file can be changed manually with a text editor. No errors will be
; displayed by vega loading the configuration.


; General preferences:
; ~~~~~~~~~~~~~~~~~~~~

; Default output format:

OUTFORMAT	PDB

; Starting residue for renumbering:

RENSTART	1

; Interaction energy calculation:
; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

; Residue name & number (format RESNAME:RESNUM):

ENERGY_RES	9999

; Cutoff distance (Amstrong):

ENERGY_CUTOFF	10.0

; Filter for energy decopmosition by residue (%):

ENERGY_FILTER	1.0

; Dielectric constant:

ENERGY_DIEL	1

; Mopac parameters:
; ~~~~~~~~~~~~~~~~~

; Default keywords:

MOPAC_DEF	AM1 PRECISE

; Charge calculation (AUTO/charge):

MOPAC_CRG	AUTO

; Peptide bond correction (AUTO/ON/OFF):

MOPAC_MMOK	AUTO

; SAS parameters:
; ~~~~~~~~~~~~~~~

; Probe radius (A):

SAS_PROBERAD	1.4

; Points density:

SAS_POINTS	10

; Shell generation:
; ~~~~~~~~~~~~~~~~~

; Box length / Sphere radius / Shell (A):

SOL_RADIUS	10.0

; Shape type (Box, Sphere, Shell):

SOL_SHAPE	BOX