Hi, I am trying to analyse my trajectory for specific salt bridges and the only program I can find is g_saltbr with the -sep command, which gives back all atom pairs that come within the set cutoff at any point in simulation time, whether they are charged and H-bond partners or not and regardless of whether they are together long enough or just glancing past each other.
This means that I am getting 80 000+ "salt bridges" in my protein, which is obviously incorrect. I cannot find any other program to analyse salt bridges, does anyone know if there is a better one? Or if there is a way to make g_saltbr's results more specific and managable. Thank you very much for your consideration. Regards, -- View this message in context: http://gromacs.5086.n6.nabble.com/Salt-bridge-analysis-tool-tp5006330.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 * 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
