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?
Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul <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 | (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/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/mailing_lists/users.php >
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