Sentence examples for using a charge calculation from inspiring English sources
Specifically, QM is employed for calculating electron orbital populations, and the populations are divided among the individual atoms using a charge calculation scheme.
The most common method for charge calculation is an application of the QM approach and afterwards the utilisation of a charge calculation scheme.
Although the optimization of AutoDock 4 scoring function was outside the scope of the current study, the fact that significantly more accurate protein-ligand complex geometry prediction is achieved using the PM6 method hints at the possibility of more accurate binding energy estimation using PM6 charge calculation as well.
The surface charge has been determined for each protein using Coulomb charge calculation.
Additionally, the weighting constants of these terms in AutoDock 4 were optimized using the Gasteiger charge calculation method; therefore, the final energy calculation is not expected to give a more accurate result using the current weighting constants in the scoring function.
It is important to note that AutoDock 4 scoring function - which is used both during and at the end of the dockings thus influencing both the geometry and binding energy estimation - was optimized using the Gasteiger charge calculation method.
This result is not surprising considering the fact that AutoDock 4 scoring function was optimized using the Gasteiger charge calculation method.
An alternative is to use empirical charge calculation methods, such as the electronegativity equalization method (EEM) [2], which is very fast and has accuracy comparable to QM.
The latter finding is not surprising because of several reasons: Although the electrostatic term for a given atom pair is greatly increased when the semi-empirical PM6 method is used for charge calculation compared to Gasteiger charge calculation, this increase is equally present for both negatively and positively charged atoms.
Goal In this case study, we would like to obtain high-quality EEM parameters for the wwPDB CCD database and based on several frequently used QM charge calculation approaches.
