Dear colleagues, I have some doubts about LIE and would like some clarifications.
While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol and a standard deviation in parentheses. How well can I use this value alone or meaningful it is by itself in comparing the binding affinity of a set of ligands (not calculating the same for the ligand-only system) ? Another query is that, to calculate the DGbind using the following formula DGbind = vdw_bound - vdw_free + Elec_bound - Elec_free Are the values calculated by -Clj tag is the value for vdw_bound or vdw_free and -Cqq is for Elec_bound or Elec_free? In another literature, this formula is further detailed DGbind_formula http://gromacs.5086.n6.nabble.com/file/n4999944/DGbind.jpg where alpha, beta and gamma values are also needed, what are these values and how to calculate them? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/LIE-using-g-lie-tp4999944.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
