[gmx-users] water in channel

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 20 09:34:01 CET 2004

On Mon, 2004-01-19 at 23:06, David L. Bostick wrote:
> Yes, Eric is right..
> Generally speaking, something like Dowser will work in more cases.
Just wanted to say that we have used Dowser in a recent paper 
[J. Biol. Chem. 279, 2147-2158 (2004)] to insert water into the pore
of Bacterio Rhodopsin. In order to get any water at all inside, we had
to reduce the energy treshold, which is hardcoded in the program, from
10 to 2.5 kcal/mol. When we did this, however, some of the crystal
waters were reproduced lending credibility to the method.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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