[gmx-users] ligand energy calculation PME simulation

[Mark Abraham]

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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