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<DIV><FONT face=Arial size=2>I tried to evaluate LR Coulomb interaction energy
for ligand and protein. My system contains<BR>membrane, ligand, TM protein
and ions. I did three reruns of my trajectory:<BR>1) leaving charges
on ligand, zeroing rest <BR>2) leaving charges on protein, zeroing rest
<BR>3) leaving charges on protein and ligand, zeroing rest.<BR>Then I
calculated LR Coulomb interaction energy for prot-lig
(Elr_c(ligand-protein)):</FONT></DIV>
<DIV> </DIV><FONT face=Arial size=2>
<DIV><BR>Elr_c(protein-ligand) = Elr_c(ligand-ligand) + Elr_c(ligand-protein)
+<BR>
Elr_c(protein-protein) <BR> in my case:</DIV>
<DIV> </DIV>
<DIV>3 = 1 + Elr_c(ligand-protein) + 2</DIV>
<DIV> </DIV>
<DIV> I also included long range corrections for each of the reruns that I
found using –rerun –debug option. <BR>Is this a right way to estimate LR
coulomb interaction energy between two molecules, my estimated energy seems
wrong 13.567.<BR> Please give me some comment on this.<BR>Thank you
in advance. </DIV>
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