OMEGA 2.4.6 (February 2012)

New features

  • Now uses an extension of the MMFF94 force field for tricoordinate boron compounds. Most compounds containing B-X bonds where X=C,N,O,S, and H are covered with the following exceptions: X=N(imine),N(sulfonamide), N(pyridinium) and N(quaternary). Also not supported are compounds in which boron is bonded to X=F,Cl,Br,I,B and Si, or makes a bond angle BYX. Compounds in which boron is a part of four-membered rings of B1CCC1 type are also not available in the current parameterization because their existence is questionable: Ab initio calculations at the MP2/6-31G** level failed to identify stable structures for them (highly polar structures in which boron is four-coordinated are formed).

Bug fixes

  • Fixed a bug where OMEGA wasn’t checking if 3D construction of fragment generation was successful.
  • Fixed a bug where output from flipper could still fail in OMEGA for missing stereo chemistry. Now the rules for required stereo chemistry are consistent.
  • Fixed a bug where setting stereo chemistry in too small of a ring could cause a crash. Now only rings greater than 7 members and only one double bond will be set with flipper.
  • Fixed a bug where OMEGA wasn’t checking if user generated fragment libraries were in OEB format. Fragment libraries must be in OEB format.
  • Fixed bugs related to nonsense values for command line parameters. User-supplied parameters must be a legal value. The ‘–help <parameter>’ command will print out the legal values.
  • Fixed a bug where SD tagged data wasn’t passed along to output molecules.

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