CHARMMRATE is a module of CHARMM for carrying out variational transition state theory (VTST) calculations to predict reaction rates and other properties of enzymatic systems. Although CHARMMRATE allows execution of POLYRATE with all existing capabilities, the present implementation is primarily intended for prediction of reaction rates for enzyme-catalyzed reactions. The procedure involves the partition of the system into a frozen bath subsystem and a dynamics primary dynamics subsystem; only the atoms of the latter subsystem are allowed to have kinetic energy in the transmission coefficient calculation.
The first application of the methods in CHARMMRATE was to the proton transfer step in the conversion of 2-phosphoglycerate to 2-phosphopyruvate by yeast enolase (1999). The first application of the method in its definitive form (EA-VTST/MT) was in conjunction with an application to liver alcohol dehydrogenase (2001). For additional descriptions of the methods, see references below.
CHARMMRATE-version 1.0/P8.1.1-C27 is the long name of version 1.0 of CHARMMRATE. It is based on version 8.1.1 of POLYRATE amd versions 27b2 and 28b1 of CHARMM. The first official release of this module was in in version 28b1 of CHARMM.
"Quantum Dynamics of Hydride Transfer in Enzyme Catalysis," C. Alhambra, J. C. Corchado, M. L. Sanchez, J. Gao, and D. G. Truhlar, Journal of the American Chemical Society 122, 8197-8203 (2000).
CHARMMRATE-version 2.0/P9.0-C28b3 is the long name of version 2.0 of CHARMMRATE. It is based on version 9.0 of POLYRATE amd version 28b3 of CHARMM. This version is currently being finalized in version 29a3 of CHARMM, which is under development by the CHARMM development group. It will be released by the CHARMM Development Group when it is ready.
"The Incorporation of Quantum Effects in Enzyme Kinetics Modeling," D. G. Truhlar, J. Gao, C. Alhambra, M. Garcia-Viloca, J. Corchado, M. L. Sánchez, and J. Villà, Accounts of Chemical Research 35, 341-349 (2002).
"Hydride Transfer by Xylose Isomerase: Mechansim and Quantum Effects,"
M. Garcia-Viloca, C. Alhambra, D. G. Truhlar, and J. Gao, Journal of Computational
Chemistry, to be published in the Peter Kollman memorial issue.
The prospective user of CHARMMRATE needs to obtain:
POLYRATE and CRATE can be obtained from their home pages: