Hi, I wanted to check how I can calculate J couplings with gromacs. And as a test I have choosen NMR ensemble of ubiquitin from this paper: "Simultaneous determination of protein structure and dynamics" Lindorff-Larsen, Nature2005
I used g_chi: g_chi -f 1XQQ.pdb -s 1XQQ.gro -g And I always end up with J values with huge SD... for example: 5.38 +/- 3.02 Hz... Is it normal?? and because of that I have very bad agreement with exp values... I tried different parametrization of Karplus eq. but SD was the same... I am missing something? Thanks a lot! best! tomek -- 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
