two questions relative to g_chi from the gmx-3.3.1 but gmx-4.0.2
uses similar code.
1) In the header of g_chi obtained using the -h option there is a
"bug" that indicates that
the phi/psi angles are not calculated as the usual C(-)-N-CA-C and N-
CA-C-N(+) definitions
but H-N-CA-C and N-CA-C-O instead, respectively.
From both the code and the comparison of the values extracted with
g_chi and VMD, it
seems that the actual correct definition is used.
From what I can recall of 3.3.1, the incorrect definitions are used
and then there is a +180 that corrects for the strange definition.
Standard:
phi: C[i-1]-N-Ca-C
psi: N-Ca-C-N[i+1]
GROMACS g_chi:
phi: H-N-Ca-C minus 180deg
psi: N-Ca-C-O minus 180deg
(http://www.gromacs.org/pipermail/gmx-users/2007-February/025927.html)
This adds noise to your date. Use g_rama instread.
2) Which Karplus equation parameterization is used to calculated the
Jcouplings?
no comment here.
Chris.
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