[gmx-users] g_chi and J coupling

Tomek Wlodarski tomek.wlodarski at gmail.com
Fri Feb 22 19:58:43 CET 2013


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!


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