[gmx-users] ligand energy calculation PME simulation

[Berk Hess]

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: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> 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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