[gmx-users] ligand energy calculation PME simulation

Antonio Coluccia antonio.coluccia at uniroma1.it
Mon Sep 7 15:09:23 CEST 2009

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 ?

Could someone help me please? Any idea will be really appreciated.

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