OMEGA provides the facility for users to select one of a number of pre-defined modes. Except for the macrocycle mode, all of the other modes share the same set of parameters. However, the default parameters vary between the various modes.
Default parameters for the various modes are described below. While the default parameters for each mode may vary, the user has the ability to modify any parameter in any mode.
The classic mode is the original customizable OMEGA interface. All the OMEGA default parameters mentioned in Optional Parameters refers to the classic mode.
For rocs, all default parameters are identical to the default parameters in classic mode except for the following changes listed below:
-maxconfs = 50
For fastrocs, all default parameters are identical to the default parameters in classic mode except for the following changes listed below:
-maxconfs = 10
For pose, all default parameters are identical to the default parameters in classic mode except for the following changes listed below:
-maxConfRange = "200,800" -rangeIncrement = 8
For dense, all default parameters are identical to the default parameters in classic mode except for the following changes listed below:
-strictstereo = false -ewindow = 15 -maxtime = 3600 -rms = 0.3, -maxrot = 20 -maxconfs = 20000
The macrocycle mode has its own set of default parameters as described in Options specific to the macrocycle mode.
OMEGA provides the facility for users to select one of a number of pre-defined force fields. The force field selected may be different for model construction and torsion search. The ability to select a force field provides a mechanism for task specificity. Some force fields may be more appropriate for solution phase ensemble generation, whilst others may excel for bioactive conformer reproduction. The following pre-defined force fields may be used as arguments to the -buildff and -searchff flags.
A file of alternate torsion rules may be specified with the -settorlib command. OMEGA will match only the first rule found for a torsion angle, and discontinue matching alternate possible rules. Thus, a correctly ordered torsion file will be arranged with the most specific patterns appearing at the top of the file, and more general patterns appearing toward the end. Simple torsion rules are composed of a single SMARTS pattern containing at least four atom expressions, followed by a listing of the torsion angles that OMEGA will sample. Each reference atom in the SMARTS pattern that is used to define the torsion angle being sampled must have a map index (numbered 1 through 4) specified that indicates the ordering of the atoms in the torsion angle. The pattern must appear all on a single line, with a carriage return separating one rule from the next. Comments in the file must be preceded with a # character. The following is an example of a simple torsion rule.
#methyl ester pattern [O:1]=[C:2]-[O:3][CH3:4] 0
More advanced rules may be included that alter the energy calculation for particular torsion angles. In these types of torsion rules, a SMARTS pattern with associated map indices is still used to define the molecular environment in which the rule is to be applied, but the sampled values appear on subsequent lines with one torsion angle per line. The first number per line indicates the torsion angle, in degrees, that OMEGA must sample. If a second number follows a torsion angle on the same line, the value is added to the total energy computed for that conformer. The following is an example of an advanced torsion rule.
#experimental structure test O=[C:1][NX3H:2][c:3]([cH,nH0])[nH:4] 0 180 10.0 <end>