Dear Gromacs Users!
I want to analyze protein-ligand polar interactions by means of g_hbond utility In particular I want to obtain some map wich include information aabout dynamics of the h bonds occurence between defined polar groups of the protein ( active site) and ligand polar atoms. For that I've defined side chains of some amino acinds as the separate group and used g_hbond on that group as well as on the ligand. As the result I've obtain correct numbers of donor and acceptors as well as average number of the h bonds along trajectory. But the map which I need ( I suppose that this is the hbmap.xpm file) represent as the long long graph with some points ( I suppose that its correspons to the different h bonds occured along that trajectory) but without any legend on that graph (e.g specified residues of the active site and corresonded atoms of the ligand). Is it possible to obtain such diagram ? 2) From Justin's tutorial I've found that the reasonable way to obtain information about dominant force mediated protein-ligand interaction in particular case is the ussage of G_energy. How from that measurements I could conclude which interaction ( e.g vdw or h-bonds) is most crussial for the ligand binding ( affinity) ? Thanks for help James -- 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
