Thanks a lot Justin for the reply !!! While calculating the Elj and Eqq values should we consider the short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in the .edr file? And for Coulomb also? Which one should we consider?
Thanks again. Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> Thanks a lot Justin for the reply. >> Yes I am going through all the relevant literature on LIE. >> Actually the lie.xvg file contains the same value of -25.4 for all the >> frames. So I am getting a straight line plot. Why is this happening? Am I >> missing out something? >> >> > If the interactions of your ligand and its receptor are stable, then there > may be no change in the energetics. I don't know anything about your > system, so I can't say anything beyond that. > > -Justin > > Thanks a lot again. >> >> Anirban >> >> >> On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Thanks a lot Justin for the reply. >> So I ran a simulation with my ligand in water for 1 ns and using >> g_energy I calculated the LG-14 and Coulomb-14 values from the >> .edr file. I supplied the average of these two values as my Elj >> and Eqq to g_lie and I got the DGbind as -25.4. Is this the >> correct way to do this? >> >> >> Again I would ask you to not rely entirely upon my advice for this. >> I have only examined the LIE method sparingly. My best answer is, >> "probably," but do read the literature on the method to be sure. >> >> >> And why am I getting only a single value of DGbind for all the >> frames captured in the .edr file? >> >> >> The lie.xvg file contains the LIE values as a function of time. >> What's printed to the screen is the average value and standard >> deviation. >> >> -Justin >> >> Thanks a lot. >> >> Anirban >> >> >> On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Thanks Justin for the reply. >> I have through the threads about g_lie, but cannot >> understand >> how to get the values for Elj and Eqq for a particular >> ligand. >> Like in my case for a system consisting of a beta2AR >> protein + >> dopamine (ligand) + POPC + water, what should be the >> values for >> Elj and Eqq? >> >> >> To obtain these (from my limited understanding), you would >> have to >> run a simulation of your ligand in water, decomposing the >> nonbonded >> energies between the ligand and solvent into LJ and Coulombic >> components. Those are your values. >> >> I should also note that simply going through the archive to >> inform >> yourself about the LIE method is insufficient. The original >> literature, and several subsequent papers (one at least >> within the >> last year, IIRC), describes the accuracy of the method and >> what it >> needs to be properly run. >> >> -Justin >> >> Thanks a lot. >> >> Anirban >> On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Hi ALL, >> >> I have run a protein + ligand (dopamine) >> simulation. Now >> I want >> to calculate the free energy of binding using >> g_lie. But >> g_lie >> asks for two values: Elj and Eqq. How or from >> where can I get >> these values for my ligand? Also, do I need to run a >> simulation >> with only the ligand? And, is there any other way >> (like >> MMGBSA >> in Amber) to calculate the free energy for my >> simulation? Any >> suggestion is welcome. >> Thanks a lot in advance. >> >> >> Go to the literature and understand what information is >> needed for >> such a simulation, and then look into the list >> archives and >> you'll >> find dozens of threads about using g_lie. >> >> -Justin >> >> >> Regards, >> >> Anirban >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> >> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. >> Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before >> posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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