Why not do a steered MD or umbrella sampling, where you start with the ligand in the binding pocket (in its correct conformation) and gradually pull it out. If done correctly, you should get a nice PMF.
> Hello! > I need to calculate the free energy of complex formation between protein A > and ligand B. I am about to simulate in solution the molecular dynamics of > A, B and AB complex separately and calculate the free energy of each > system using g_lie. Then, I suppose, deltaG = G(AB) - (G(A) + G(B)). > Is it a correct algorithm? Or maybe it's better to use "slow-growth" > method (whith lambda = 1 for the absence of ligand in the binding pocket) > to calculate the difference between G(AB) and G(A)? > Thank you! > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
