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

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 24 13:59:43 CET 2009

Neha Gandhi wrote:
> 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.
Please check recent papers from the Aqvist group.

> Many thanks,
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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