[gmx-users] g_chi and torsional angles
Sandor Lovas
SandorLovas at creighton.edu
Thu Dec 1 18:27:51 CET 2005
Than I should say the angle definitions are wrong in g_chi, they do not
follow conventions, therefore, results could be misleading:
I copied here part of a structure file and the corresponding output
(chi.log)
Structure:
1ALA N 1 3.562 2.218 2.878 0.5075 -0.4009 -0.2929
1ALA H1 2 3.641 2.235 2.937 0.5503 -0.1968 -0.4035
1ALA H2 3 3.548 2.121 2.860 -0.4536 -0.7485 2.0694
1ALA H3 4 3.585 2.261 2.790 1.8632 -1.0614 -0.2916
1ALA CA 5 3.436 2.258 2.942 0.5631 -0.0157 -0.4098
1ALA CB 6 3.455 2.406 2.977 -0.2534 -0.0442 0.1426
1ALA C 7 3.306 2.236 2.865 0.1307 -0.4194 0.4205
1ALA O 8 3.292 2.152 2.776 -0.2003 0.1358 -0.0557
2ALA N 9 3.200 2.296 2.918 0.2834 0.1087 0.1264
2ALA H 10 3.202 2.333 3.010 0.9805 -1.2027 0.6552
2ALA CA 11 3.076 2.321 2.842 0.1590 0.8241 0.5482
2ALA CB 12 2.969 2.364 2.943 -0.4890 -0.0032 0.2365
2ALA C 13 3.103 2.431 2.740 0.4232 0.2444 -0.0133
2ALA O 14 3.189 2.518 2.756 0.2789 0.4016 -0.0868
3GLY N 15 3.020 2.449 2.637 -0.1869 0.1175 0.4532
3GLY H 16 2.955 2.380 2.605 -0.1420 0.4072 -0.2725
3GLY CA 17 3.035 2.565 2.548 -0.5698 -0.0023 0.2228
3GLY C 18 3.044 2.528 2.400 -0.4774 0.2780 0.1559
3GLY O 19 3.132 2.456 2.353 -0.5339 0.1656 0.2364
4ASP N 20 2.959 2.597 2.323 -0.4545 0.1756 0.0327
4ASP H 21 2.887 2.659 2.353 -0.9106 0.3980 -1.4441
4ASP CA 22 2.949 2.590 2.177 -0.1954 0.5615 -0.0061
4ASP CB 23 2.799 2.585 2.146 -0.1315 0.2244 -0.2770
4ASP CG 24 2.724 2.712 2.189 0.3699 0.4550 -0.0780
4ASP OD1 25 2.674 2.779 2.097 0.1515 -0.1099 -0.3718
4ASP OD2 26 2.737 2.754 2.306 0.6242 0.3487 -0.0585
4ASP C 27 3.022 2.709 2.112 0.0970 0.0899 -0.5616
4ASP O 28 3.143 2.714 2.132 0.0381 -0.0732 -0.1616
5TYR N 29 2.950 2.794 2.040 -0.4454 -0.2776 -0.4590
5TYR H 30 2.851 2.802 2.052 -0.5294 -0.6510 -0.8740
5TYR CA 31 3.004 2.879 1.933 -0.2098 0.1104 -0.0357
5TYR CB 32 2.894 2.891 1.827 -0.2574 -0.0793 -0.0072
5TYR CG 33 2.876 2.774 1.730 0.3700 -0.3455 0.1969
5TYR CD1 34 2.816 2.654 1.767 0.5287 -0.3086 0.5728
5TYR HD1 35 2.753 2.645 1.854 -1.7704 0.0222 -0.9670
5TYR CD2 36 2.938 2.789 1.606 0.3357 -0.2619 0.1894
5TYR HD2 37 2.986 2.881 1.577 0.1702 -0.5658 -1.1095
5TYR CE1 38 2.819 2.549 1.676 -0.1451 -0.1527 0.3476
5TYR HE1 39 2.758 2.466 1.708 1.3566 -0.1348 3.8080
5TYR CE2 40 2.944 2.680 1.520 0.2326 -0.3585 0.3032
5TYR HE2 41 2.977 2.689 1.417 -1.0434 -2.2192 -0.3202
5TYR CZ 42 2.882 2.560 1.553 -0.7032 0.0552 0.0820
5TYR OH 43 2.866 2.467 1.456 0.4939 0.4361 -0.4984
5TYR HH 44 2.780 2.420 1.474 -2.1323 4.9834 0.3245
5TYR C 45 3.042 3.012 1.998 -0.0187 -0.1974 0.4917
5TYR O 46 2.951 3.081 2.044 -0.2640 0.1173 -0.4352
6TYR N 47 3.169 3.015 2.038 0.3531 0.1647 -0.6888
6TYR H 48 3.232 2.938 2.027 -1.0865 -1.2089 0.2993
6TYR CA 49 3.240 3.129 2.097 -0.4699 0.2177 0.2191
6TYR CB 50 3.265 3.096 2.245 0.0316 -0.1360 0.0573
6TYR CG 51 3.128 3.101 2.312 -0.1894 0.2743 -0.4176
6TYR CD1 52 3.057 2.985 2.342 0.0967 0.3673 0.6427
6TYR HD1 53 3.096 2.888 2.314 -1.3609 -0.2707 0.7406
6TYR CD2 54 3.087 3.229 2.348 -0.7178 0.0609 -0.2409
6TYR HD2 55 3.141 3.316 2.314 0.1695 -0.5419 -0.4301
6TYR CE1 56 2.938 2.999 2.412 0.1973 -0.5481 1.0083
6TYR HE1 57 2.870 2.916 2.425 0.2410 -0.4729 1.7892
6TYR CE2 58 2.974 3.240 2.427 -0.4928 0.3655 0.0422
6TYR HE2 59 2.941 3.338 2.459 -0.5823 1.1613 -2.3012
6TYR CZ 60 2.901 3.125 2.458 -0.2228 -0.0175 -0.7255
6TYR OH 61 2.792 3.135 2.539 0.2389 0.0429 -0.1030
6TYR HH 62 2.756 3.228 2.547 1.1846 0.4551 -0.4195
6TYR C 63 3.376 3.142 2.029 -0.6233 -0.0397 -0.1371
6TYR O 64 3.425 3.049 1.965 0.3830 0.1292 0.3743
7NH2 N 65 3.427 3.264 2.020 0.4141 -0.4216 0.4585
7NH2 H1 66 3.379 3.345 2.055 1.0105 -0.0315 0.4032
7NH2 H2 67 3.504 3.269 1.956 -2.2804 2.6664 -2.9527
Part of chi.log:
Residue ALA1
Angle [ AI, AJ, AK, AL] #tr/ns S^2D
--------------------------------------------
Phi [ 2, 1, 5, 7] 27.55 0.00
Psi [ 1, 5, 7, 8] 6.90 0.87
Residue ALA2
Angle [ AI, AJ, AK, AL] #tr/ns S^2D
--------------------------------------------
Phi [ 10, 9, 11, 13] 10.20 0.73
Psi [ 9, 11, 13, 14] 9.40 0.79
Residue GLY3
Angle [ AI, AJ, AK, AL] #tr/ns S^2D
--------------------------------------------
Phi [ 16, 15, 17, 18] 9.00 0.52
Psi [ 15, 17, 18, 19] 10.40 0.15
Residue ASP4
Angle [ AI, AJ, AK, AL] #tr/ns S^2D
--------------------------------------------
Phi [ 21, 20, 22, 27] 0.90 0.89
Psi [ 20, 22, 27, 28] 0.30 0.88
Chi1[ 20, 22, 23, 24] 0.25 0.88
Chi2[ 22, 23, 24, 25] 7.90 0.00
Residue TYR5
Angle [ AI, AJ, AK, AL] #tr/ns S^2D
--------------------------------------------
Phi [ 30, 29, 31, 45] 2.15 0.85
Psi [ 29, 31, 45, 46] 4.75 0.74
Chi1[ 29, 31, 32, 33] 0.70 0.53
Chi2[ 31, 32, 33, 34] 0.25 0.31
Residue TYR6
Angle [ AI, AJ, AK, AL] #tr/ns S^2D
--------------------------------------------
Phi [ 48, 47, 49, 63] 10.25 0.84
Psi [ 47, 49, 63, 64] 7.75 0.21
Chi1[ 47, 49, 50, 51] 1.30 0.44
Chi2[ 49, 50, 51, 52] 0.50 0.00
For example: for ALA2 the phi should be 7, 9, 11, 13 : C(i-1), N(i),
CA(i), C(i)
you could check for the other residues and all phi, psi are wrongly
defined.
Sandor
--
___________________________________________________________________________
Dr. Sandor Lovas, Associate Professor | Phone: 402-280-5753
Department of Biomedical Sciences | Fax: 402-280-2690
Creighton University | http://bif1.creighton.edu
2500 California Plaza, |
Omaha, NE 68178, USA |
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