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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