[gmx-users] Re: Re: g_chi -omega
Dongsheng Zhang
dong at pampas.chem.purdue.edu
Tue Nov 29 16:24:38 CET 2005
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.
>
> Message: 2
> Date: 29 Nov 2005 00:47:41 -0500
> From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> Subject: [gmx-users] g_chi -omega
> To: gmx-users at gromacs.org
> Message-ID: <1133243260.32559.56.camel at pampas.chem.purdue.edu>
> Content-Type: text/plain
>
> 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?
>
>
>
> PPII-PRO.PDB:
>
> ATOM 1 N PRO 2 3.553 1.514 -1.245 1.00
> 0.00
> ATOM 2 CA PRO 2 4.313 2.450 -2.183 1.00
> 0.00
> ATOM 3 C PRO 2 4.115 2.148 -3.667 1.00
> 0.00
> ATOM 4 O PRO 2 3.990 0.946 -4.012 1.00
> 0.00
> ATOM 5 CB PRO 2 5.789 2.270 -1.860 1.00
> 0.00
> ATOM 6 CG PRO 2 5.822 0.779 -1.484 1.00
> 0.00
> ATOM 7 CD PRO 2 4.548 0.586 -0.655 1.00
> 0.00
> ATOM 8 H PRO 2 2.857 1.014 -1.816 1.00
> 0.00
> ATOM 9 HA PRO 2 3.992 3.469 -2.028 1.00
> 0.00
> ATOM 10 1HB PRO 2 6.384 2.410 -2.780 1.00
> 0.00
> ATOM 11 2HB PRO 2 6.044 2.871 -0.979 1.00
> 0.00
> ATOM 12 1HG PRO 2 5.602 0.098 -2.322 1.00
> 0.00
> ATOM 13 2HG PRO 2 6.750 0.622 -0.918 1.00
> 0.00
> ATOM 14 1HD PRO 2 4.190 -0.452 -0.756 1.00
> 0.00
> ATOM 15 2HD PRO 2 4.743 0.888 0.386 1.00
> 0.00
> ATOM 16 N PRO 3 4.077 3.120 -4.560 1.00
> 0.00
> ATOM 17 CA PRO 3 3.887 2.960 -6.067 1.00
> 0.00
> ATOM 18 C PRO 3 5.118 2.438 -6.804 1.00
> 0.00
> ATOM 19 O PRO 3 6.248 2.799 -6.390 1.00
> 0.00
> ATOM 20 CB PRO 3 3.570 4.348 -6.605 1.00
> 0.00
> ATOM 21 CG PRO 3 4.413 5.223 -5.661 1.00
> 0.00
> ATOM 22 CD PRO 3 4.211 4.571 -4.289 1.00
> 0.00
> ATOM 23 HA PRO 3 3.086 2.263 -6.266 1.00
> 0.00
> ATOM 24 1HB PRO 3 3.978 4.445 -7.626 1.00
> 0.00
> ATOM 25 2HB PRO 3 2.507 4.566 -6.447 1.00
> 0.00
> ATOM 26 1HG PRO 3 5.501 5.086 -5.772 1.00
> 0.00
> ATOM 27 2HG PRO 3 4.007 6.240 -5.734 1.00
> 0.00
> ATOM 28 1HD PRO 3 5.097 4.749 -3.657 1.00
> 0.00
> ATOM 29 2HD PRO 3 3.272 4.939 -3.847 1.00
> 0.00
> ATOM 30 N PRO 4 4.998 1.634 -7.843 1.00
> 0.00
> ATOM 31 CA PRO 4 6.139 1.041 -8.668 1.00
> 0.00
> ATOM 32 C PRO 4 6.812 2.033 -9.613 1.00
> 0.00
> ATOM 33 O PRO 4 6.094 2.913 -10.152 1.00
> 0.00
> ATOM 34 CB PRO 4 5.524 -0.067 -9.510 1.00
> 0.00
> ATOM 35 CG PRO 4 4.125 0.514 -9.775 1.00
> 0.00
> ATOM 36 CD PRO 4 3.731 1.134 -8.431 1.00
> 0.00
> ATOM 37 HA PRO 4 6.911 0.664 -8.013 1.00
> 0.00
> ATOM 38 1HB PRO 4 6.061 -0.134 -10.473 1.00
> 0.00
> ATOM 39 2HB PRO 4 5.430 -0.976 -8.903 1.00
> 0.00
> ATOM 40 1HG PRO 4 4.125 1.419 -10.403 1.00
> 0.00
> ATOM 41 2HG PRO 4 3.491 -0.329 -10.078 1.00
> 0.00
> ATOM 42 1HD PRO 4 3.043 1.980 -8.597 1.00
> 0.00
> ATOM 43 2HD PRO 4 3.319 0.351 -7.776 1.00
> 0.00
> ATOM 44 N PRO 5 8.108 1.969 -9.858 1.00
> 0.00
> ATOM 45 CA PRO 5 8.905 2.893 -10.776 1.00
> 0.00
> ATOM 46 C PRO 5 8.691 2.634 -12.266 1.00
> 0.00
> ATOM 47 O PRO 5 8.515 1.446 -12.637 1.00
> 0.00
> ATOM 48 CB PRO 5 10.373 2.643 -10.461 1.00
> 0.00
> ATOM 49 CG PRO 5 10.343 1.144 -10.120 1.00
> 0.00
> ATOM 50 CD PRO 5 9.064 0.987 -9.291 1.00
> 0.00
> ATOM 51 HA PRO 5 8.628 3.921 -10.597 1.00
> 0.00
> ATOM 52 1HB PRO 5 10.971 2.779 -11.379 1.00
> 0.00
> ATOM 53 2HB PRO 5 10.655 3.213 -9.568 1.00
> 0.00
> ATOM 54 1HG PRO 5 10.092 0.492 -10.972 1.00
> 0.00
> ATOM 55 2HG PRO 5 11.264 0.935 -9.559 1.00
> 0.00
> ATOM 56 1HD PRO 5 8.661 -0.032 -9.414 1.00
> 0.00
> ATOM 57 2HD PRO 5 9.273 1.257 -8.245 1.00
> 0.00
>
> --
> Dongsheng Zhang <dong at pampas.chem.purdue.edu>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 29 Nov 2005 09:03:34 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] g_chi -omega
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <438C0B56.4020606 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
--
Dongsheng Zhang <dong at pampas.chem.purdue.edu>
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