SZYBKI 1.5.0

New features

  • Starting from the current release, certain classes of divalent selenium compounds can be handled by Szybki. Currently only some compounds in which selenium is bonded to the hydrogen or carbon atoms can be processed. Those compounds include selenols (RSeH) and selenides (RSeR1) in which Se is bonded to alkyl or aromatic carbon atoms, with the exception when Se makes a bond with alkyl C which belongs to the 3- or 4-membered ring.
  • Previous Szybki releases attempted to assign the “closest” MMFF94 atom type to those atoms for which a unique MMFF94 type could not be found. Starting from the 1.5.0 release this feature is removed, so consequently the input molecules containing such atoms will not be processed.
  • Ligand RMSD which is reported in the log file, can optionally refer to the heavy atoms only. The new option used for that purpose is -heavy_rms.
  • Entropy calculations of a ligand in different environments can be performed based on the methods described in the recent paper of Wlodek et. al. ([Wlodek-2010]). This is done with the option -entropy described in the section 4.1 of this manual.
  • Default VdW protein-ligand potential used for the optimization of a ligand inside the protein binding site is precalculated in the form of a lookup table. This is done for the purpose of speed. The exact VdW protein-ligand potential can be used with the option -exact_vdw.

Bug fixes

  • Memory leak in ligand torsion optimization inside the partially flexible protein receptor was removed.