[gmx-users] Topology from semiempiricaly optimized structure
Semen Esilevsky
yesint4 at yahoo.com
Tue Jun 15 12:57:12 CEST 2004
Dear Daan van Aalten,
Don't you think that your reply is a bit offensive?
Why do you think that all people who have problems are
just stupid? Even if somebody misunderstood something
it is not a reason to say "you are stupid, don't write
to this list anymore". In my case I just can't
understand your reply:
> Ahhhh .. so you are the person submitting PDB files
> with all Z-coordinates
> set to 0.000.
Who said you this??????? All Z-coordinates are in
place. It is NOT flat! Here is PDB file:
============
HETATM 1 C 1 0.000 0.000 0.000
HETATM 2 C 2 1.372 0.000 0.000
HETATM 3 C 3 2.252 1.167 0.000
HETATM 4 C 4 1.711 2.436 0.255
HETATM 5 C 5 -0.785 -1.250 -0.009
HETATM 6 C 6 0.036 -2.478 -0.040
HETATM 7 O 7 2.099 -1.180 0.022
HETATM 8 O 8 -0.647 1.211 0.039
HETATM 9 C 9 2.249 -3.518 -0.020
HETATM 10 C 10 1.654 -4.762 -0.056
HETATM 11 C 11 0.252 -4.888 -0.091
HETATM 12 C 12 -0.543 -3.747 -0.095
HETATM 13 C 13 3.628 1.069 -0.257
HETATM 14 C 14 4.430 2.194 -0.250
HETATM 15 C 15 3.891 3.471 0.011
HETATM 16 C 16 2.509 3.564 0.264
HETATM 17 O 17 -2.008 -1.276 0.009
HETATM 18 C 18 1.433 -2.366 -0.015
HETATM 19 H 19 0.623 2.521 0.434
HETATM 20 H 20 -1.566 1.059 -0.149
HETATM 21 H 21 3.343 -3.421 -0.002
HETATM 22 H 22 2.285 -5.661 -0.071
HETATM 23 C 23 -0.354 -6.243 -0.229
HETATM 24 H 24 -1.642 -3.829 -0.133
HETATM 25 H 25 4.095 0.102 -0.475
HETATM 26 H 26 5.506 2.083 -0.454
HETATM 27 H 27 2.047 4.541 0.471
HETATM 28 N 28 4.699 4.637 -0.083
HETATM 29 C 29 4.196 5.925 0.482
HETATM 30 C 30 4.139 7.000 -0.588
HETATM 31 C 31 6.185 4.506 -0.032
HETATM 32 C 32 6.824 5.088 -1.280
HETATM 33 H 33 3.186 5.788 0.929
HETATM 34 H 34 4.856 6.248 1.315
HETATM 35 H 35 3.853 7.965 -0.149
HETATM 36 H 36 5.116 7.135 -1.084
HETATM 37 H 37 3.408 6.764 -1.372
HETATM 38 H 38 6.573 5.022 0.873
HETATM 39 H 39 6.480 3.438 0.076
HETATM 40 H 40 7.918 5.069 -1.197
HETATM 41 H 41 6.552 4.526 -2.183
HETATM 42 H 42 6.519 6.136 -1.444
HETATM 43 N 43 -1.125 -6.719 1.026
HETATM 44 C 44 -2.502 -6.042 1.081
HETATM 45 C 45 -3.315 -6.449 2.306
HETATM 46 C 46 -4.659 -5.740 2.308
HETATM 47 C 47 -5.480 -6.140 3.524
HETATM 48 C 48 -6.826 -5.433 3.530
HETATM 49 C 49 -7.650 -5.831 4.744
HETATM 50 C 50 -8.997 -5.126 4.753
HETATM 51 C 51 -9.818 -5.520 5.960
HETATM 52 C 52 -0.345 -6.414 2.286
HETATM 53 C 53 -1.334 -8.220 0.913
HETATM 54 H 54 0.438 -6.994 -0.451
HETATM 55 H 55 -1.051 -6.261 -1.097
HETATM 56 H 56 -2.359 -4.931 1.050
HETATM 57 H 57 -3.062 -6.297 0.153
HETATM 58 H 58 -3.456 -7.555 2.316
HETATM 59 H 59 -2.750 -6.215 3.238
HETATM 60 H 60 -4.510 -4.641 2.296
HETATM 61 H 61 -5.217 -5.978 1.379
HETATM 62 H 62 -5.630 -7.239 3.537
HETATM 63 H 63 -4.924 -5.903 4.453
HETATM 64 H 64 -6.678 -4.334 3.517
HETATM 65 H 65 -7.383 -5.670 2.601
HETATM 66 H 66 -7.799 -6.930 4.758
HETATM 67 H 67 -7.094 -5.595 5.674
HETATM 68 H 68 -8.847 -4.028 4.739
HETATM 69 H 69 -9.552 -5.362 3.823
HETATM 70 H 70 -10.789 -5.009 5.963
HETATM 71 H 71 -10.015 -6.600 5.981
HETATM 72 H 72 -9.309 -5.263 6.898
HETATM 73 H 73 -0.971 -6.596 3.182
HETATM 74 H 74 0.563 -7.032 2.357
HETATM 75 H 75 -0.034 -5.355 2.307
HETATM 76 H 76 -2.068 -8.559 1.670
HETATM 77 H 77 -1.731 -8.491 -0.079
HETATM 78 H 78 -0.396 -8.776 1.066
CONECT 1 2 5 8
CONECT 2 1 3 7
CONECT 3 2 4 13
CONECT 4 3 16 19
CONECT 5 1 6 17
CONECT 6 5 12 18
CONECT 7 2 18
CONECT 8 1 20
CONECT 9 10 18 21
CONECT 10 9 11 22
CONECT 11 10 12 23
CONECT 12 6 11 24
CONECT 13 3 14 25
CONECT 14 13 15 26
CONECT 15 14 16 28
CONECT 16 4 15 27
CONECT 17 5
CONECT 18 6 7 9
CONECT 19 4
CONECT 20 8
CONECT 21 9
CONECT 22 10
CONECT 23 11 43 54 55
CONECT 24 12
CONECT 25 13
CONECT 26 14
CONECT 27 16
CONECT 28 15 29 31
CONECT 29 28 30 33 34
CONECT 30 29 35 36 37
CONECT 31 28 32 38 39
CONECT 32 31 40 41 42
CONECT 33 29
CONECT 34 29
CONECT 35 30
CONECT 36 30
CONECT 37 30
CONECT 38 31
CONECT 39 31
CONECT 40 32
CONECT 41 32
CONECT 42 32
CONECT 43 23 44 52 53
CONECT 44 43 45 56 57
CONECT 45 44 46 58 59
CONECT 46 45 47 60 61
CONECT 47 46 48 62 63
CONECT 48 47 49 64 65
CONECT 49 48 50 66 67
CONECT 50 49 51 68 69
CONECT 51 50 70 71 72
CONECT 52 43 73 74 75
CONECT 53 43 76 77 78
CONECT 54 23
CONECT 55 23
CONECT 56 44
CONECT 57 44
CONECT 58 45
CONECT 59 45
CONECT 60 46
CONECT 61 46
CONECT 62 47
CONECT 63 47
CONECT 64 48
CONECT 65 48
CONECT 66 49
CONECT 67 49
CONECT 68 50
CONECT 69 50
CONECT 70 51
CONECT 71 51
CONECT 72 51
CONECT 73 52
CONECT 74 52
CONECT 75 52
CONECT 76 53
CONECT 77 53
CONECT 78 53
END
============
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