[gmx-users] Re: the output of do_dssp
Justin A. Lemkul
jalemkul at vt.edu
Wed May 26 16:35:45 CEST 2010
Hsin-Lin Chiang wrote:
> Hi, Justin:
>
> I post my coordinate with protein translated by trjconv
> By this gro file, I get 0 structure and 13 coils.
>
Analyze both chains separately using index groups. I would also encourage you
to file a bugzilla about this issue. If you consider residues 1-6 and 7-12
separately, you get sensible output (6 residues in each). For some reason, if
the two chains are combined and considered as a continuous structure, you get an
extra residue, probably related to the termini.
-Justin
> regards,
> Hsin-Lin
>
> Generated by trjconv : Protein in water t= 0.00000
> 144
> 1LEU N 1 2.499 1.707 2.735 -0.1664 0.1749 0.5034
> 1LEU H1 2 2.496 1.753 2.824 -0.0517 -2.4571 1.9862
> 1LEU H2 3 2.456 1.619 2.755 0.1871 0.0557 0.7811
> 1LEU H3 4 2.591 1.691 2.698 -0.0836 0.9027 0.3938
> 1LEU CA 5 2.419 1.772 2.633 -0.3054 -0.5208 0.2431
> 1LEU CB 6 2.277 1.809 2.687 0.1445 -0.1872 -0.2452
> 1LEU CG 7 2.202 1.686 2.731 -0.2024 0.3028 0.1044
> 1LEU CD1 8 2.063 1.737 2.778 0.2195 0.2407 0.1571
> 1LEU CD2 9 2.197 1.583 2.615 0.2120 -0.5339 0.1770
> 1LEU C 10 2.479 1.897 2.572 0.1063 -0.1920 0.0451
> 1LEU O 11 2.483 2.008 2.627 0.2017 -0.4490 0.0233
> 2TYR N 12 2.493 1.882 2.437 -0.1877 -0.3169 -0.5678
> 2TYR H 13 2.446 1.812 2.384 0.6045 -1.4218 0.1228
> 2TYR CA 14 2.568 1.987 2.363 -0.2499 0.5688 -0.4543
> 2TYR CB 15 2.589 1.933 2.224 0.6646 -0.2988 -0.3037
> 2TYR CG 16 2.641 2.031 2.122 0.0017 0.2452 -0.1870
> 2TYR CD1 17 2.772 2.065 2.121 -0.4594 -0.2211 -0.0739
> 2TYR HD1 18 2.841 2.029 2.196 -0.1936 2.1660 0.9115
> 2TYR CD2 19 2.561 2.096 2.031 0.6321 -0.0604 0.5143
> 2TYR HD2 20 2.454 2.077 2.025 0.6551 0.1338 -0.9454
> 2TYR CE1 21 2.827 2.158 2.032 -0.1241 0.2352 -0.6043
> 2TYR HE1 22 2.935 2.169 2.027 -0.0121 -0.2184 0.4867
> 2TYR CE2 23 2.607 2.183 1.935 -0.7318 -0.3641 0.2984
> 2TYR HE2 24 2.537 2.240 1.874 2.4629 1.6445 -1.8271
> 2TYR CZ 25 2.744 2.223 1.938 -0.9702 -0.5296 0.3816
> 2TYR OH 26 2.796 2.320 1.854 0.1652 0.2056 -0.1630
> 2TYR HH 27 2.714 2.370 1.829 -0.0067 -0.1509 -0.3161
> 2TYR C 28 2.492 2.121 2.359 -0.9847 -0.4718 -0.5034
> 2TYR O 29 2.369 2.129 2.344 0.1513 0.3775 -0.1130
> 3GLN N 30 2.564 2.228 2.385 -0.2495 0.1552 0.8649
> 3GLN H 31 2.647 2.221 2.441 -0.1774 -3.6419 0.5524
> 3GLN CA 32 2.519 2.362 2.357 0.6342 0.0752 -0.4227
> 3GLN CB 33 2.615 2.451 2.432 0.3037 -0.2198 0.6973
> 3GLN CG 34 2.569 2.596 2.453 -0.2200 0.0688 -0.5109
> 3GLN CD 35 2.556 2.690 2.327 0.9953 0.3411 -0.2090
> 3GLN OE1 36 2.640 2.694 2.240 -0.9468 -0.2495 -0.6126
> 3GLN NE2 37 2.449 2.761 2.321 -0.4839 0.0971 -0.2517
> 3GLN HE21 38 2.384 2.757 2.397 -0.8822 0.9806 -0.5342
> 3GLN HE22 39 2.443 2.818 2.239 1.3155 1.4839 0.4945
> 3GLN C 40 2.501 2.401 2.207 0.2212 -0.2300 0.2782
> 3GLN O 41 2.596 2.416 2.125 -0.3813 -0.0351 0.0925
> 4LEU N 42 2.377 2.427 2.177 -0.1825 0.0192 -0.2668
> 4LEU H 43 2.302 2.432 2.243 1.4715 -0.4825 1.7638
> 4LEU CA 44 2.342 2.451 2.033 0.2037 0.0368 -0.1113
> 4LEU CB 45 2.230 2.360 1.985 -0.4049 -0.4174 -0.1918
> 4LEU CG 46 2.193 2.374 1.838 0.7678 -0.3161 0.4261
> 4LEU CD1 47 2.243 2.255 1.755 0.7379 0.9397 0.6576
> 4LEU CD2 48 2.041 2.401 1.828 -0.2357 0.6221 -0.0518
> 4LEU C 49 2.300 2.600 2.014 0.1156 -0.7579 0.2678
> 4LEU O 50 2.183 2.641 2.032 0.0777 -0.1884 0.5428
> 5GLU N 51 2.402 2.676 1.977 0.1065 0.0801 -0.1886
> 5GLU H 52 2.499 2.669 2.001 -0.3871 0.9888 2.3980
> 5GLU CA 53 2.367 2.813 1.924 -0.4424 0.3677 0.0128
> 5GLU CB 54 2.465 2.914 1.989 -0.0708 -0.1784 0.3292
> 5GLU CG 55 2.431 3.059 2.017 0.0676 0.0058 -0.4907
> 5GLU CD 56 2.423 3.160 1.897 -0.1295 0.3354 0.1946
> 5GLU OE1 57 2.530 3.183 1.835 0.3233 -0.4874 0.7816
> 5GLU OE2 58 2.313 3.196 1.854 0.6508 -0.0618 0.6984
> 5GLU C 59 2.391 2.807 1.773 0.6638 -0.1591 -0.6210
> 5GLU O 60 2.500 2.836 1.726 -0.0179 -0.4997 -0.0116
> 6ASN N 61 2.278 2.810 1.704 -0.1838 -0.0571 0.1524
> 6ASN H 62 2.193 2.843 1.747 -1.7146 -1.5150 -1.5696
> 6ASN CA 63 2.278 2.779 1.562 -0.0805 -0.8216 0.6185
> 6ASN CB 64 2.200 2.652 1.531 -0.5886 -0.3894 -0.0808
> 6ASN CG 65 2.285 2.528 1.538 -0.1917 0.0598 0.1828
> 6ASN OD1 66 2.367 2.510 1.624 -0.1949 0.0958 0.2131
> 6ASN ND2 67 2.262 2.432 1.453 -0.0713 0.3669 0.1154
> 6ASN HD21 68 2.176 2.451 1.407 -1.5107 -0.4210 2.3205
> 6ASN HD22 69 2.323 2.356 1.434 -0.8178 -0.7718 1.9579
> 6ASN C 70 2.223 2.893 1.484 -0.0883 0.1244 -0.1837
> 6ASN O1 71 2.111 2.941 1.505 -0.2557 -0.4837 -0.1041
> 6ASN O2 72 2.313 2.953 1.419 -0.5561 0.0660 0.4455
> 7LEU N 73 1.111 2.804 2.186 0.3062 -0.5955 -0.0550
> 7LEU H1 74 1.174 2.856 2.129 0.2303 -0.3221 0.1077
> 7LEU H2 75 1.019 2.834 2.164 0.0461 -1.9085 -0.8807
> 7LEU H3 76 1.126 2.815 2.284 0.4122 -2.4532 0.1866
> 7LEU CA 77 1.119 2.659 2.168 0.4439 0.3219 0.1920
> 7LEU CB 78 1.065 2.580 2.290 0.1893 0.7407 0.4674
> 7LEU CG 79 1.085 2.429 2.286 -0.3605 0.1679 0.1372
> 7LEU CD1 80 1.237 2.384 2.277 0.3311 -0.4092 0.3485
> 7LEU CD2 81 1.017 2.370 2.407 -0.0510 0.3161 -0.2535
> 7LEU C 82 1.054 2.605 2.036 -0.5425 0.2570 -0.0982
> 7LEU O 83 0.932 2.605 2.009 0.5537 -0.1985 0.5728
> 8TYR N 84 1.145 2.540 1.969 -0.4316 0.1827 -0.1087
> 8TYR H 85 1.242 2.554 1.991 -0.7733 1.5318 0.6050
> 8TYR CA 86 1.130 2.452 1.849 -0.2270 -0.1076 -0.8653
> 8TYR CB 87 1.171 2.536 1.732 -0.3024 0.2551 0.3837
> 8TYR CG 88 1.164 2.479 1.587 0.1807 -0.6891 -0.4950
> 8TYR CD1 89 1.074 2.383 1.547 0.4151 -0.4168 0.3628
> 8TYR HD1 90 0.992 2.374 1.617 0.5971 0.1568 0.6583
> 8TYR CD2 91 1.277 2.493 1.505 -0.0975 -0.2077 -0.0153
> 8TYR HD2 92 1.361 2.557 1.531 -0.2867 -0.1036 0.3676
> 8TYR CE1 93 1.086 2.309 1.432 0.1265 0.0409 0.4196
> 8TYR HE1 94 1.027 2.218 1.421 -1.4249 1.1394 -0.9377
> 8TYR CE2 95 1.283 2.426 1.381 0.0193 0.3605 -0.7563
> 8TYR HE2 96 1.371 2.444 1.319 1.0230 1.0179 0.8015
> 8TYR CZ 97 1.188 2.333 1.343 0.3042 0.2754 0.1067
> 8TYR OH 98 1.192 2.280 1.219 0.1044 0.0574 0.4195
> 8TYR HH 99 1.116 2.216 1.208 1.8924 -2.0623 -0.4187
> 8TYR C 100 1.204 2.322 1.856 -0.1562 0.9065 0.6949
> 8TYR O 101 1.325 2.322 1.869 -0.4089 -0.5515 0.0368
> 9GLN N 102 1.127 2.211 1.859 -0.1041 -0.9648 -0.0726
> 9GLN H 103 1.028 2.216 1.866 -0.0213 -0.9055 1.7059
> 9GLN CA 104 1.190 2.079 1.876 0.2408 0.0804 0.0683
> 9GLN CB 105 1.124 2.016 1.997 0.0726 -0.3357 0.2763
> 9GLN CG 106 1.197 2.060 2.124 0.2194 0.1012 0.3405
> 9GLN CD 107 1.130 1.997 2.248 -0.4181 0.1293 -0.6010
> 9GLN OE1 108 1.023 2.036 2.292 -0.2051 -0.1900 0.1232
> 9GLN NE2 109 1.181 1.887 2.292 -0.3581 0.6878 0.3867
> 9GLN HE21 110 1.241 1.834 2.233 -1.1830 0.3448 -0.1534
> 9GLN HE22 111 1.143 1.840 2.372 1.6496 1.8603 2.1410
> 9GLN C 112 1.170 2.005 1.745 0.3840 -0.5229 0.3516
> 9GLN O 113 1.062 2.017 1.689 -0.7908 -0.0106 0.2891
> 10LEU N 114 1.285 1.964 1.689 -0.2339 0.2740 0.5923
> 10LEU H 115 1.369 1.993 1.735 -0.0502 1.9043 -0.6774
> 10LEU CA 116 1.305 1.904 1.557 0.5504 0.0009 -0.0746
> 10LEU CB 117 1.355 2.002 1.454 -0.5733 -0.0394 0.5322
> 10LEU CG 118 1.409 1.954 1.320 0.2018 -1.1430 0.6864
> 10LEU CD1 119 1.291 1.896 1.244 0.3218 -0.6662 -0.0855
> 10LEU CD2 120 1.484 2.066 1.245 -0.4351 -0.3578 0.1148
> 10LEU C 121 1.385 1.770 1.568 0.6352 -0.4683 0.3665
> 10LEU O 122 1.504 1.785 1.584 -0.7087 -0.4803 -0.6135
> 11GLU N 123 1.318 1.657 1.551 -0.7690 0.3531 -0.3536
> 11GLU H 124 1.227 1.661 1.509 -0.5836 0.1171 -0.7863
> 11GLU CA 125 1.384 1.528 1.573 0.2213 0.0654 -0.5702
> 11GLU CB 126 1.301 1.427 1.658 -0.3925 -0.1676 -0.0424
> 11GLU CG 127 1.305 1.477 1.799 -0.1339 -0.0701 -0.8319
> 11GLU CD 128 1.212 1.399 1.895 -0.2284 0.6451 -0.1694
> 11GLU OE1 129 1.093 1.425 1.899 -0.0761 0.2707 0.5798
> 11GLU OE2 130 1.261 1.304 1.963 0.1320 0.1556 0.1656
> 11GLU C 131 1.429 1.461 1.448 -0.6174 -0.7459 0.7565
> 11GLU O 132 1.351 1.393 1.378 0.0471 0.2366 0.3611
> 12ASN N 133 1.557 1.481 1.416 -0.1975 0.0440 0.6480
> 12ASN H 134 1.617 1.512 1.490 1.1138 1.0357 -0.7510
> 12ASN CA 135 1.619 1.413 1.302 0.2119 0.3743 -0.0748
> 12ASN CB 136 1.659 1.527 1.202 0.0785 -0.0388 -0.5075
> 12ASN CG 137 1.609 1.494 1.061 -0.5358 0.5714 -0.1604
> 12ASN OD1 138 1.493 1.518 1.038 0.3125 -0.1729 0.0001
> 12ASN ND2 139 1.687 1.435 0.971 -0.4423 0.5272 -0.1120
> 12ASN HD21 140 1.777 1.401 0.995 -0.4365 1.0512 0.6434
> 12ASN HD22 141 1.652 1.412 0.880 0.6790 -1.4313 -0.1016
> 12ASN C 142 1.732 1.324 1.357 -0.0019 -0.4376 0.2441
> 12ASN O1 143 1.798 1.364 1.456 -0.5732 0.5215 0.5206
> 12ASN O2 144 1.758 1.218 1.296 0.3692 -0.2774 0.0431
> 4.16562 4.16562 4.16562
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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