5 Default settings (prefs file)
VEGA (command line) starts reading the preference file in order to set the default parameters. This file is placed in Data directory, it's called prefs and it's in ASCII format editable as a normal text file. Each entry has a keyword with one or more parameters. A semicolon (;) placed in the first column indicates that the line is a remark. Please remember that VEGA doesn't print any warning about incorrect parameters or syntax errors in the prefs file. VEGA ZZ doesn't use this method to set the default parameters. In the following table are reported all available keywords:
Keyword |
Description |
ENERGY_CUTOFF |
Cut-off distance to
speed-up the interaction energy evaluation (see f [FORMAT] option). |
ENERGY_DIEL |
Dielectric constant
value (see f [FORMAT] option). |
ENERGY_FILTER |
Filter for energy
decomposition by residue (see f [FORMAT] option). |
ENERGY_RES |
Residue name and number
(format RESNAME:RESNUM) for interaction energy evaluation (see e[NAME:NUM] option). |
LANGUAGE | Default language (see
language localization page): |
MAXATMINFO | It's the maximum atom
number that the info file format (see f [FORMAT] option)
can manage for the calculation of extra information. This number is in function of your
CPU power. |
MOPAC_CRG |
Charge attribution with
Mopac keyword CHARGE. It can be set to AUTO (the total charge is calculated by
atomic charges) or to a positive or negative integer value. |
MOPAC_DEF |
Mopac default keywords
(see k[KEYWORDS] option). |
MOPAC_MMOK |
MMOK is a Mopac keyword
needed to introduce a correction factor when in a molecule there are peptidic
(amidic)
bonds. The argument can be: |
OUTFORMAT |
Output format. |
RENSTART |
Starting residue for
renumbering (see a[RES_NUM]
option). |
SAS_POINTS |
The default point
density for molecular surface calculations (see s[POINTS]
). |
SAS_PROBERAD |
The default probe
radius for calculation of the molecular surface accessible to solvent (see f[FORMAT] option). |
SOL_RADIUS |
Box length /Sphere
radius / Layer thickness (see h[SHELL RAD
SHAPE] ). |
SOL_SHAPE |
Shape type (BOX,
SPHERE, SHELL): |
VOL_DENSITY | Dot density for volume calculations (see -m[KEYWORDS] and -f info ). e.g. VOL_DENSITY 10 |
For more information about prefs file, see the APPENDIX B.