SZYBKI 1.5.1

Bug fixes

  • Ligand optimization in the active site with the use of the flag -protein_elec set at PB ended prematurely. This problem has been fixed.
  • In the previous (1.5.0) release the entropy calculation of the protein-bound ligand worked only when a single molecule in the ligand input file was present. In the case when the ligand input file contained two or more molecules, the calculation was performed for the first molecule and died on next one with segmentation fault. This bug is fixed.
  • Calculated entropy of the protein-bound ligand was underestimated by up to 0.5 kcal/mol due to the underestimation of the buried protein surface area upon binding. This error is corrected in the current release.
  • Using options: -exact_vdw and -protein_elec set at PB resulted in minimization with Coulomb and VdW potential only. This has been corrected in the current release.
  • Parameter file was written without the user command line flags. This bug is fixed.
  • A tiny memory leak in the calculations of protein-ligand interaction has been removed.
  • Two subsections in documentation has been added. That includes the theory of entropy estimation adopted by SZYBKI and several examples of command line SZYBKI executions.