Abstract:
Calculations of the electronic structure of molecules by quantum
chemical methods long ago are performed using supercomputers. Today they are
conducted on the leader of the TOP500 supercomputer list and will be realized on
the first exaflops supercomputer in the USA.
A brief review of modern quantum chemistry methods and their supercomputer application for calculations of primarily large molecules shows the need
for accelerated approximation techniques to realize the possibilities of such
computations. The need is especially urgent for massive calculations of such giant
biomolecules as protein-ligand docking complexes. For this, we have proposed
and implemented software that gives excellent acceleration at an acceptable
accuracy of approximation calculations for calculating the molecular integrals
of non-empirical methods of quantum chemistry. For massive calculations of
docking complexes using semiempirical methods, we propose and implement a
new technique in software. It uses some localizations of ligand-protein interactions
due to the formation of groups from a full set of ligands.
This method allows us to achieve acceleration by orders of magnitude and
also intended for use in future non-empirical calculations. The proposed methods
and programs for the necessary massive calculations of docking complexes
naturally fit into a batch job processing system and can be used in a GRID
environment. Such a GRID system arises on the computing resources of the
Yaroslavl State University and the Institute of Organic Chemistry of the Russian
Academy of Sciences on the base of EGI standardized UMD 4 software.
Key words and phrases:high speed quantum chemical methods, docking complexes, GRID.