CHARMMRATE Home Page

CHARMMRATE

Mireia Garcia-Viloca, Cristobal Alhambra, Jose Corchado, Maria Luz Sanchez, J. Villa, Jiali Gao, and Donald G. Truhlar

Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, U.S.A.

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-2.0 manual

CHARMMRATE-1.0 abstract
CHARMMRATE-1.0 manual

CHARMM documentation

CHARMM is described in the following paper:
 
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comp. Chem., 4(2), 1983, 187-217.


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.
 

The authors are Cristobal Alhambra, Jose Corchado, Maria Luz Sanchez, J. Villa, Jiali Gao, and Donald G. Truhlar.  CHARMMRATE-1.0 is described in the following papers:
 "Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton-Transfer Reaction," C. Alhambra, J. Gao, J. C. Corchado, J. Villà, and D. G. Truhlar, Journal of the American Chemical Society 121, 2253-2258 (1999).

"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 authors are Mireia Garcia-Viloca, Cristobal Alhambra, Jose Corchado, Maria Luz Sanchez, J. Villa, Jiali Gao, and Donald G. Truhlar.  CHARMMRATE-2.0 is described in the following papers:
 
"Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase," C. Alhambra, J. Corchado, M. L. Sánchez, M. Garcia-Viloca, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B 105, 11326-11340 (2001).

"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.
 

Publications based on using the CHARMMRATE module of CHARMM should give the CHARMM, POLYRATE, and CHARMMRATE citations as recommended in either the CRATE manual or the CHARMMRATE manual.

To obtain CHARMMRATE:

The prospective user of CHARMMRATE needs to obtain:

1. CHARMM (version 28b1 or later should contain CHARMMRATE as a module)
2. POLYRATE-version 9.0 or later
3. CRATE-version 9.0.1

 
A CHARMM license and the CHARMM program should be obtained from an academic or commercial CHARMM licenser.
 
from Harvard (non-commercial users):
          The CHARMM Development Project
          Dept. of Chemistry and Chemical Biology
          12 Oxford Street
          Harvard University
          Cambridge, MA 01238
          marci@tammy.harvard.edu

from Accelrys:
 

www.accelrys.com/about/msi.html


POLYRATE and CRATE can be obtained from their home pages:
 

POLYRATE:  POLYRATE Home Page
CRATE:         CRATE Home Page

Links to other pages of interest:

Don Truhlar's Home Page
Density Functionals from the Truhlar Group
Source Code of CF22D
Computational Chemistry at the University of Minnesota
Minnesota Supercomputing Institute
Department of Chemistry at the University of Minnesota