[gmx-users] g_chi -omega

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 29 09:03:34 CET 2005

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 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

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