5. Setting default parameters (prefs file)
For each run, VEGA reads a preference file in order to set the default parameters. This file is placed in Data directory, called prefs, is in ASCII format and can be modified with a text editor. Each entry has a keyword with one or more parameters. A semicolon (;) placed in the first column of a line indicates that the line is a remark. Please remember that VEGA do not print any warning about incorrect parameter or syntax errors in the prefs file . 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 petidic (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.