David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 28 09:28:23 CET 2004
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
Did you fix it in CVS as well? (i.e. is the fix in 3.2)?
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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