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).
e.g. ENERGY_CUTOFF 10

ENERGY_DIEL

Dielectric constant value (see –f [FORMAT] option).
e.g. ENERGY_DIEL 1

ENERGY_FILTER

Filter for energy decomposition by residue (see –f [FORMAT] option).
e.g. ENERGY_FILTER 1

ENERGY_RES

Residue name and number (format RESNAME:RESNUM) for interaction energy evaluation (see –e[NAME:NUM] option).
e.g. ENERGY_RES 9999

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.
e.g. MOPAC_CRG AUTO

MOPAC_DEF

Mopac default keywords (see –k[KEYWORDS] option).
e.g. MOPAC_DEF AM1 PRECISE

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:
AUTO: VEGA recognizes the presence of amidic bonds and automatically switches on or off the MMOK Mopac function.
ON: MMOK is always switched on.
OFF: MMOK is always switched off.
e.g. MOPAC_MMOK AUTO

OUTFORMAT

Output format.
e.g. OUTFORMAT PDB

RENSTART

Starting residue for renumbering (see –a[RES_NUM] option).
e.g. RENSTART 1

SAS_POINTS

The default point density for molecular surface calculations (see –s[POINTS] ).
e.g. SAS_POINTS 10

SAS_PROBERAD

The default probe radius for calculation of the molecular surface accessible to solvent (see –f[FORMAT] option).
e.g. SAS_PROBERAD 1.4

SOL_RADIUS

Box length /Sphere radius / Layer thickness (see –h[SHELL RAD SHAPE] ).
e.g. SOL_RADIUS 10

SOL_SHAPE

Shape type (BOX, SPHERE, SHELL):
e.g. SOL_TYPE BOX

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.