[gmx-users] Drug-Enzyme tutorial- LIE energies in gromacs

Alexandre Suman de Araujo asaraujo at if.sc.usp.br
Tue Mar 24 14:52:27 CET 2009


There are several works dealing with LIE parametrization to many kinds 
of systems.

In the original formulation of the method, the alpha and beta parameters 
were considered the same for all studied systems. However, with the 
application of the method in many cases, it was observed the exigence of 
different LIE parameters set for different systems. This is obtained, in 
general, with the methodology which defines a training and a test sets 
of solutes.

I'll point you some references that can help you with this subject:

1 - Aqvist, J., Calculation of absolute binding free energies for 
charged ligands and effects of long-range electrostatic interactions. J 
Comput Chem 1996, 17, (14), 1587-1597.
2 - Aqvist, J.; Hansson, T., On the validity of electrostatic linear 
response in polar solvents. J Phys Chem-Us 1996, 100, (22), 9512-9521.
4 - Almlof, M.; Aqvist, J.; Smalas, A. O.; Brandsdal, B. O., Probing the 
effect of point mutations at protein-protein interfaces with free energy 
calculations. Biophys J 2006, 90, (2), 433-442.
5 - Stjernschantz, E.; Marelius, J.; Medina, C.; Jacobsson, M.; 
Vermeulen, N. P. E.; Oostenbrink, C., Are automated molecular dynamics 
simulations and binding free energy calculations realistic tools in lead 
optimization? An evaluation of the linear interaction energy (LIE) 
method. Journal of Chemical Information and Modeling 2006, 46, (5), 
6 - de Araujo, A. S.; Sonoda, M. T.; Piro, O. E.; Castellano, E. E., 
Development of new Cd2+ and Pb2+ Lennard-Jones parameters for liquid 
simulations. J. Phys. Chem. B 2007, 111, (9), 2219-2224.

Other references can be found therein.

Best regards

Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *

Neha Gandhi escreveu:
> Dear GMX-users,
> In the Gromacs Drug/Enzyme complex solvation tutorial by John E. 
> Kerrigan , in the end they mention about the LIE calculation. The 
> g_lie program uses LIE equation with default scaling factors a=0.18 
> and b=0.50 . In the tutorial it is mentioned that For example,  b = 
> 0.33 is preferred for polar solutes (drugs) like sugars. What is the 
> reference for these values for polar solutes i.e. sugars.? I would 
> appreciate if there is any example of such calculation done in gromacs.
> Many thanks,
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
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