Hi,
The LIE approach might work in vacuum (although the vacuum itself is a gross
approximation).
But I don't see how you can do that in solution.
The only way to get a reasonable estimate is by doing free-energy calculations,
either PMF or growing the ligand.
Another possibility could be implicit solvent models, which will be available
in Gromacs 4.1.
Berk
> Date: Tue, 8 Sep 2009 12:19:00 +1000
> From: [email protected]
> To: [email protected]
> Subject: Re: [gmx-users] ligand energy calculation PME simulation
>
> Antonio Coluccia wrote:
> > Hi All
> >
> > I have problems with the binding energy. I have done a series of dynamics
> > simulation on a series of analogues compounds using PME and i would like to
> > compute the binding energy of all the analyzed compounds.
> >
> > I have read a lot on the mail archive but it is still unclear. I have done
> > a dynamics of the complex (protein+ligand) and I repeated the same analysis
> > for the ligand in solution. I am not using g_lie since I used PME. I'm
> > using the aveage values for Coul and LJ energy but the resulting binding
> > energy is not real. What I have to do to avoid PME contribution. I am doing
> > same mistakes ?
>
> Either avoid using PME, or do a real free energy calculation (which will
> only be feasible for a very small ligand), or do an implicit solvation
> estimate using (e.g.) APBS.
>
> Mark
>
> > Could someone help me please? Any idea will be really appreciated.
> >
> > Ant.
> >
> >
> >
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