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<DIV><FONT face=Arial size=2>Thank you for comment. <BR>Could you please explain
why do I need more reruns.<BR>I’m looking for interaction ligand-protein, not
ligand-system.<BR> In may case:<BR>1 = LR (lig-lig) …
terms for rest, and prot = 0 <BR>2 = LR (prot-prot) …. terms for rest, and
lig = 0<BR>3 = LR (lig-lig) + LR (lig-prot) + LR (prot-prot)</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>LR (lig-prot) = 3 -1 -2 </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>For every run, for groups mentioned above, rest (
which means other groups than protein and ligand) , I assigned charges =
zero.<BR>The LR coulomb energy calculated using g_energy gives total LR coulomb
energy for all the groups with non zero charges, so it doesn’t involve any terms
that came from the rest groups with charges equal zero. <BR>Could you
please explain why do I need more reruns, I guess I missed
something.<BR>Thank you in advance. </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2> <BR>On Wed, 2005-05-04 at 19:37 +0200, Michal
Kolinski wrote:<BR>> I tried to evaluate LR Coulomb interaction energy for
ligand and<BR>> protein. My system contains<BR>> membrane, ligand,
TM protein and ions. I did three reruns of my<BR>> 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<BR>> (ligand-protein)):<BR>> <BR>> <BR>>
Elr_c(protein-ligand) = Elr_c(ligand-ligand) + Elr_c(ligand-protein)
+<BR>>
Elr_c(protein-protein) </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>principle is right, but where is the membrane and
solvent? You probably<BR>need more reruns..'</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2><BR>> in my
case:<BR>> <BR>> 3 = 1 + Elr_c(ligand-protein) +
2<BR>> <BR>> I also included long range corrections for each
of the reruns that I<BR>> found using –rerun –debug option. <BR>> Is
this a right way to estimate LR coulomb interaction energy between<BR>> two
molecules, my estimated energy seems wrong 13.567.<BR>> Please
give me some comment on this.<BR>> Thank you in advance. <BR>>
<BR>> <BR></FONT></DIV></BODY></HTML>