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