[gmx-users] g_chi -omega

[David van der Spoel]

Dongsheng Zhang wrote:
> Hi,
> 
> I have checked the mailing archive, It seems no one complained about the
> calculation of omega angle. I have a PDB file for polyproline with trans
> conformation. But when I use 
> 
> g_chi -s PPII-PRO.PDB -f PPII-PRO.PDB -omega
> 
> to calculate the omega angle. I got zero. To my understanding, the omega
> should be 180 for trans conformation. Could anyone tell me where I made
> a mistake?
> 

It seems that your angles are indeed Cis. The definition of omega is 
Ca-N-C-O which is indeed 0 degrees in the conformation you sent to the 
list. Where did you get the coordinates from?


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++