Table 1 OMEGA parameters modified or non-default during conformer generation

-startfact

20, 50

Determines the fragment sampling rate for determination of fragment conformation [default = 20].

-buildff ^a

MMFF94s MMFF94s_NoEstat MMFF94s_Trunc

Specifies the type of a molecular force field used in the model building step [default = MMFF94s_NoEstat]

-searchff ^a

MMFF94s MMFF94s_NoEstat MMFF94s_Trunc

Specifies the type of a molecular force field used in the torsion search step [default = MMFF94s_NoEstat].

-ewindow

integers between 1 and 30

Determines the size of the energy window [default = 10.0].

(1) In the model building step: determines the maximum energy range of a ring system.

(2) In the torsion search step: determines the maximum energy range of a conformer relative to that of a global minimum conformer.

-MaxConfsGen

100,000

Controls the maximum number of fully constructed conformers that OMEGA will attempt to build [default = 30,000].

-MaxConfs

100,000

Controls the maximum number of conformations to be retained [default = 20,000].

-MaxRotors

15

Controls the maximum number of rotatable bonds in a molecule. If a molecule has more rotatable bonds than this cutoff, OMEGA will not search for conformers [default = 12].

-MaxSearchTime

180

Limits the maximum amount of time (in seconds) spent generating conformers for each molecule [default = 30].

-DefaultRMSD

0.0

Controls the threshold of the RMS distance to determine duplicate conformations. The value of 0.0 indicates that the duplicate detection is skipped [default = 0.8].