APPENDIX B VEGA prefs file
This is an example of VEGA prefs file. This file must be placed
in Data directory.
; ******************************************** ; **** VEGA V2.2.0 - Preferences **** ; **** (c) 1997-2008, 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 Italiano ; Default output format: OUTFORMAT PDB2 ; Overlapping tolerance for connecctivity calculation (%) CONNTOL 20.0 ; 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 ; **** 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