On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > lina wrote: >> >> Hi, >> >> For group A, b, C. >> >> It's no doubt can get hb forming number between A-b, b-C. b-(A or C). >> >> But I don't know how to get the number of residues of b forming both >> with A and B at the same time. namely b-A&C, not with AC group. >> > > There's no direct way to do it, but from the output files of g_hbond it can > be done. You'd need the .xpm files of A-C and B-C hydrogen bonds, and write > some script that parses the .xpm files, and whenever there is an entry of > A-C in the same frame as B-C, then you have a hydrogen bond mediated between > the two. There's lots of discussion in the list archive about water-mediated > hydrogen bonds that is likely applicable here.
Thanks, I will try. > > Note that if you're using g_hbond in version 4.5, there is an important bug > that was fixed just yesterday: > > http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html I noticed yesterday and recompiled the gromacs already. Thanks for reminding. > > -Justin > >> Thanks, >> -- >> Best Regards, >> >> lina >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- Best Regards, lina -- 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
