[gmx-users] gromacs result

[David van der Spoel]

Maik Goette wrote:
> Right, but I can just warn anyone.
> Trying to use TI on a docked structure is insanity...
> The docked structure is an approximation in its best case (more likely 
> its simply crap). Applying a free energy calculation towards such a 
> structure will give you everything...but sure not the the correct free 
> energy of binding....except you are very lucky....IF you are that lucky, 
> play lottery instead and enjoy life ;)
> 
> In fact it's (citating Mark) another expensive random number generator...

I think you're exaggerating a bit. Docking works quite well if you do it 
correctly, that is many (>=100) tries.
See my website below for some useful publications on docking...

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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