OMEGA 2.5.1

(May 2013)

New features

  • FILTER is now completely bundled into the OMEGA package. The manuals have been consolidated into this single manual and FILTER has taken on the OMEGA version number.

  • An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled.

  • A -warts option has been added to flipper.

Major bug fixes

  • Now using -fixsmarts without -fixfile will rematch for every input structure. Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixfile will continue to match against the fixfile and use that match for the entire calculation.

  • Partial ring matching with -fixsmarts or -fixfile could cause a crash. Now only full ring systems may be specified and any attempt at matching a partial ring system will fail gracefully.

  • Planar molecules could have problems sprouting hydrogens when using -fromCT false because OMEGA was treating them as 2D. Now OMEGA will assume that planar molecules are properly defined 3D coordinates in this situation.

  • Stereochemistry at the attachment points of rings with four or less atoms could be lost. Now stereochemistry is saved for rings of all sizes.

  • A bug has been fixed where exceptionally long torsion rules could get cutoff early.

  • A bug has been fixed where older TK licenses in the license file could cause the OMEGA application to fail. [Case #13466]

Minor bug fixes

  • Only 3D coordinates were being cleared in FLIPPER. Now 2D coordinates are cleared as well.

  • Fragment generation during an OMEGA calculation with strictfrags parameter enabled could yield slightly different fragments than the MakeFraglib app. This has been corrected for consistency.

  • Tags for rotor compression are no longer attached to the output molecules when rotoroffsetcompress is false. It was discovered that these tags confuse VIDA when they are attached but not used.

  • The torsion library has been updated with better angles for a biphenyl torsion. The entry for 90 degrees has been removed and +/-30 degrees has been added.

  • FILTER has been fixed to no longer have an atom order dependence when setting a pH model.

Other changes

  • PVM (parallel virtual machine) is no longer supported. OpenMPI version 1.6 is supported on all platforms. The -mpi_np and -mpi_hostfile flags are now used to run OMEGA and makefraglib in MPI mode. These new flags replace the oempirun script.

  • This will be the last release to support SuSe 10.