Discovery Studio 2.1 Updates - Details

Update 2 (version 2.1.2)

This update addresses the same issues that were addressed in Update 1 (version 2.1.1) and includes additional enhancements and corrections.


The following enhancements and corrections are included:

  • Full compatibility with Pipeline Pilot 7.5.2 is provided. Specifically:
    • issues that could cause the Refine Docked Proteins (RDOCK), Align Multiple Sequences, and Flexible Docking protocols to fail are resolved.
    • a problem that could cause certain simulation protocols to fail because properties could not be succesfully extracted from the CHARMm output file has been fixed.
  • A memory issue when running Dock Ligands (LigandFit) and Score Ligand Poses protocols that resulted in losing some results is resolved.
  • Terminal oxygen atoms are correctly placed after inserting missing residues into protein chains.
  • Correct mapping of certain customized features in the Feature Mapping protocol is now performed.
  • The C-alpha chirality issue when running Loop Refinement protocol using the CHARMm all atom forcefield is resolved.
  • An issue resulting in the incorrect bonding of structures produced by the Loop Refinement protocol for multi-chain proteins with disulfide bridges is resolved.
  • The Screen Library protocol now always groups the results appropriately and returns multiple .sd files instead of a single file.
  • Creation of large pharmacophore databases has been improved on Windows. A problem whereby some hits were not returned in the results has also been addressed. This correction may require re-indexing of Catalyst databases; the search protocol will indicate if this is necessary.

Update 1 (version 2.1.1)

This update addresses a critical license issue affecting the Calculate Molecular Properties, Calculate Energy (QM-MM), and Minimization (QM-MM) protocols.


This update (2.1.1) addresses a critical license issue with certain protocols that make use of the DMol3 server. Without this update, DMol3 will stop functioning after 31 October 2008, which will cause the following errors:

  • The Calculate Molecular Properties protocol will appear to succeed, but if the calculation of density functional QM properties have been requested, the generated .sd file will show errors for these properties.
  • The Calculate Energy (QM-MM) and Minimization (QM-MM) protocols will fail with an error. The DMol3 output file will contain the error message "This version has expired".

All Discovery Studio 2.1 Updates