Hi Leila, I've done this with g_hbond and g_bond. If you search the forums there is a perl script available from Justin Lemakul that will do this for you. You can do it manually too if you have only a few to look at. Its a little tricky but a lot easier than traj conversion. :) I was able to get % residence, average bond length and std dev of length but I had to use ndx files with just the 3 atoms in them. It's tedious so if you have a lot of bonds check out the perl script.
Oliver On 7 December 2010 10:56, leila karami <karami.lei...@gmail.com> wrote: > Dear Oliver Grant > > thanks for your attention. > > I want to use amber tool for hydrogen bond analysis especially (water > mediated hydrogen bonds and residence time and occupation of them). > > -- > > Leila Karami > Ph.D. student of Physical Chemistry > K.N. Toosi University of Technology > Theoretical Physical Chemistry Group > > > > -- > 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 >
-- 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
