[gmx-users] phi / psi values using g_chi

[chris.neale at utoronto.ca]

> 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.