[gmx-users] Re: Re: g_chi -omega

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 29 18:50:28 CET 2005

Dongsheng Zhang wrote:
> Dear David,
> Thank you very much for your reply. When I use vmd to visualize this
> peptide (PPII-PRO.PDB), I think it is trans conformation because two
> C-alphas connected by an amide bond are at both sides of the amide bond.
> I am confused why you think it is cis conformation. Please give me more
> details. I got this PDB file from:
> http://www.cryst.bbk.ac.uk/pps97/assignments/projects/szabo/proline.htm
>>From this website, you can find that the author also thinks this peptide
> is trans conformation.'

You're right. The definition in the program is incorrect and you have to 
add 180 degrees. I'll fix it before 3.3.1

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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