Szybki TK 1.6.0

New features

  • The algorithm for entropy estimation has been improved, specifically the calculation of vibrational entropy. It can now handle molecules with up to 2000 atoms. The previous limit was about 200 atoms.
  • Entropy calculation of protein-bound ligands has been modified. This change refers to the partial desolvation entropy of the protein receptor. In the previous version, eq. 26 in Wlodek-2010 had been used to evaluate the fraction of ligand exposed to the solvent. Recent unpublished data has shown that a much more accurate estimation can be achieved by using the direct surface calculation with Spicoli TK. This change was shown to be better at reproducing binding entropies.
  • Method SetSolventModel now takes a dielectric constant as a second argument. Its default value is 80. In the previous versions dielectric constant was assumed to be 80 and the user could not change its value.
  • Badly defined input molecules with very small distances between atoms (< 1e-3 A) that could generate infinite initial forces are now detected and no attempt is made to optimize such molecules. A warning “Geometry of the input protein or conformation is badly defined!” is issued so the user is forced to correct the geometry of the input molecules.
  • A capability of calculating solution entropy for monoatomic ions like Na::math`^+` or F::math`^-` and noble gases is added.
  • Documentation for three libraries: opt, mmff and molpotential, which in the past were called CASE, was added.

Bug fixes

  • Estimation of entropy with the quasi-Newton method returned differing results (up to 6%) on different platforms. The problem was due to numerical-instability in the calculation of second derivatives. This problem has been eliminated in the current release with the use of a more stable method for line minimization (a backtrack line search).