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

[David van der Spoel]

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.
________________________________________________________________________
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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