David van der Spoel
spoel at xray.bmc.uu.se
Mon May 10 11:58:52 CEST 2004
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 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
More information about the gromacs.org_gmx-users