[gmx-developers] g_lie

[David van der Spoel]

On Tue, 2004-01-27 at 17:47, Anton Feenstra wrote:
> Tivadar Orban wrote:
> 
> > Hi,
> > Is there a chance to add in g_lie a third term (gamma*<DSASA>) in
> > calculation of binding free energy as suggested by Jorgensen in:
> > "Binding Affinities for Sulfonamide Inhibitors with Human Thrombin Using
> > Monte Carle Simulations with a Linear Response Method" D.K. Jones-Hertzog,
> > W. Jorgensen, J. Med. Chem. 1997, 40,1539-1549.
> 
> Sure, the source is right there ;-)
> 
> You can of course get the relevant raw energy numbers from the g_lie output,
> and the sasa from, e.g., g_sas, and combine things yourself with your own
> alpha's, beta's and gamma's in, e.g., an awk script (or excell sheet, brrrr).
> 
> Note, also, that the distributed version of g_lie in Gromacs 3.1.4 has a bug
> that makes it virtually unusable. I posted a fix quite a while ago on the
> list (don't remember if it was the users or the developers list). Search the
> archives.

Did you fix it in CVS as well? (i.e. is the fix in 3.2)?
-- 
David.
________________________________________________________________________
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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