APPENDIX B - VEGA prefs file

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

; ********************************************
; ****      VEGA V3.2.3 - Preferences     ****
; **** (c) 1997-2023, 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. All fields are case-insensitive.


; **** General preferences ****
;
; Language:
; (ignored by AmigaOS)

LANGUAGE        Auto

; Default output format:

OUTFORMAT	PDB2

; Overlapping tolerance for connecctivity calculation (%)

CONNTOL         20.0

; Starting residue for renumbering:

RENSTART	1

; **** Interaction energy calculation ****
;
; Contact distance for score calculation 

ENERGY_CONTDIST 2.5

; Cutoff distance (Amstrong):

ENERGY_CUTOFF	10.0

; Filter for energy decopmosition by residue (%):

ENERGY_FILTER	1.0

; Dielectric constant:

ENERGY_DIEL	1

; **** Info format ****
;
; Max atom number for calculation of extra information:
; Surface, volume, logP, etc.

MAXATMINFO      5000

; **** Mopac format ****
;
; Default keywords:

MOPAC_DEF	AM1 PRECISE GEO-OK

; 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

; Dot density:

SAS_POINTS	10

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

SOL_RADIUS	10.0

; Shape type (Box, Sphere, Shell):

SOL_SHAPE	BOX

; **** Volume calculation ****
;
; Dot density for cubic Angstrom

VOL_DENSITY     12

; **** HyperDrive parameters ****
;
; Number of CPUs used by HyperDrive (0 = all installed CPUs)

MAXCPU              0

; **** OpenCL ****
;
; Device type:
; None = OpenCL disabled
; Auto = Automatic detection
; Default = default device
; Accelerator = generic accelerator (e.g. IBM Cell Broadband Engine)
; CPU = generic CPU with SSE3 support (specific driver required)
; GPU = Graphic Processing Unit
;
; For the CPU device, a specific driver must be installed (e.g. included in the
; AMD Stream package).

OCLDEVTYPE         Auto

; **** XTC compression ****
;
; Number of digits after the point (from 1 to 8)

XTCPREC 3