3.3 Torsion Library Format

A file of alternate torsion rules may be specified with the -torlib 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>

				OMEGA C++ Toolkit

				OMEGA C++ Toolkit