Dear colleagues, Thanks for opening up this topic. I also 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 we use this value alone or meaningful it is by itself, not calculating the same for the ligand alone, in comparing the binding affinity of a set of ligands? 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 http://gromacs.5086.n6.nabble.com/file/n4999924/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/Linear-Interaction-energy-calculations-tp4999882p4999924.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
