Hi, I am intending to calculate binding affinity using Linear Interaction method (LIE method) for which I need to perform two simulations for given ligand both in free and bound states and get the values of Electrostatic and Van der Waals Interaction energies of the ligand. I have done simulation of free state of ligand. As Peptide (Chain C) of complex is the ligand, I could not understand how this is to be specified under energy-grps option in mdp for my system (as it is done in protein -ligand complex gromacs tutorial by specifying protein, JZ4(name of the ligand)).
Any help will be highly appreciated. Thanks in advance. Regards, Rajitha. -- 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
