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Hi,<br><br>The LIE approach might work in vacuum (although the vacuum itself is a gross approximation).<br>But I don't see how you can do that in solution.<br>The only way to get a reasonable estimate is by doing free-energy calculations,<br>either PMF or growing the ligand.<br><br>Another possibility could be implicit solvent models, which will be available in Gromacs 4.1.<br><br>Berk<br><br>> Date: Tue, 8 Sep 2009 12:19:00 +1000<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] ligand energy calculation PME simulation<br>> <br>> Antonio Coluccia wrote:<br>> > Hi All<br>> > <br>> > 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.<br>> > <br>> > 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 ?<br>> <br>> Either avoid using PME, or do a real free energy calculation (which will <br>> only be feasible for a very small ligand), or do an implicit solvation <br>> estimate using (e.g.) APBS.<br>> <br>> Mark<br>> <br>> > Could someone help me please? Any idea will be really appreciated.<br>> > <br>> > Ant.<br>> > <br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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