[gmx-users] g_chi -omega
Dongsheng Zhang
dong at pampas.chem.purdue.edu
Tue Nov 29 06:47:41 CET 2005
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>
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