[gmx-users] g_chi

[David van der Spoel]

On Mon, 2004-05-10 at 11:45, Marieke van den Bosch wrote:
> Dear gromacs developers and users, 
> 
> a problem occured when looking at the flexibility
> of my system using g_chi. phi and psi angles of
> certain aminoacids are perfectly stable, the angle
> vs time plot shows no changes. The output file
> chi.log however gives values for the number of
> transitions per ns in the order of 20 upto 97! The
> order parameters look fine, see below.
> 
> Residue ILE7
>  Angle [   AI,   AJ,   AK,   AL]  #tr/ns  S^2D  
> --------------------------------------------
>    Phi [   52,   51,   53,   58]   38.91    0.91
>    Psi [   51,   53,   58,   59]    6.25    0.93
>  Omega [   50,   49,   51,   53]    0.62    0.94
>    Chi1[   51,   53,   54,   55]    0.00    0.98
>    Chi2[   53,   54,   55,   57]   65.31    0.71
> 
> 
> How is a dihedral transition defined?

It's written in the help text (g_chi -h):
A log file (argument -g) is also written. This contains
(a) information about the number of residues of each type.
(b) The NMR 3J coupling constants from the Karplus equation.
(c) a table for each residue of the number of transitions between
rotamers per nanosecond,  and the order parameter S2 of each dihedral.
(d) a table for each residue of the rotamer occupancy.
All rotamers are taken as 3-fold, except for omegas and chi-dihedrals to
planar groups (i.e. chi2 of aromatics asp and asn, chi3 of glu and gln,
and chi4 of arg), which are 2-fold. "rotamer 0" means that the dihedral
was not in the core region of each rotamer. The width of the core region
can be set with -core_rotamer

So for Phi angles the dihedral is three fold, that means if you're
outside the range of -120 to 0 (-60 being the minimum for e.g. helices)
a transition is registered. IIRC it doesn't have to go all the way to
the next minimum.


> 
> 
> Best regards, 
> 
> Marieke van den Bosch.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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