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 named 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 shown all available keywords:

 

Keyword Description
ENERGY_CONTDIST Distance used to determine if the ligand is in contact with a receptor residue (see -f [FORMAT] option).
e.g. ENERGY_CONTDIST 2.5

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
LANGUAGE

Default language (see language localization page):
AUTO: Set automatically your preferred language (AmigaOS and Win32 only).
type_of_language: Set the specified language.
e.g. LANGUAGE italiano
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.
e.g. MAXATMINFO 500

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 peptidic (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
OCLDEVTYPE

Set the OpenCL device type. The argument can be: NONE (acceleration disabled), AUTO (automatic detection), DEFAULT (default device), Accelerator (generic accelerator), CPU (generic CPU with SSE3 support) and GPU (Graphic Processing Unit).

OUTFORMAT

Output format.
e.g. OUTFORMAT PDB

RENSTART

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

SAS_POINTS

Default point density for molecular surface calculations (see -s[POINTS] ).
e.g. SAS_POINTS 10

SAS_PROBERAD

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
XTCPREC Number of digits after the point (from 1 to 8) used for the compression of XTC trajectories.

e.g. XTCPREC 3

For more information about prefs file, see the APPENDIX B.