Szybki TK 1.5.0¶
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]).
New methods added to the public API are:
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 new method:
when boolean parameter passed is
falsecauses switching to the default form of the protein-ligand VdW. The function:
allows the querying of which form of the VdW potential is used.
Two functions have been added to the public API in szybki.h. The first new function allows the use of conformation-dependent AM1BCC charges for every conformation in the calculation of PB and Sheffield solvation energies, for protein-ligand Coulomb interactions, and in entropy calculations.
The second function returns
trueif AM1BCC are being calculated for every conformation,
In a special situation of ligand optimization in the protein binding site with the use of the electrostatics model determined by the
OEProteinElectrostatics.ExactCoulomb, constant, when the optimization was preceded by the Zap binding calculations with the same protein and the same ligand, Coulombic interaction resulted in zero value. This bug has been fixed.