[gmx-developers] g_lie

[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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