[gmx-users] Topology from semiempiricaly optimized structure
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Tue Jun 15 13:15:28 CEST 2004
Hi Semen
My E_mail certainly did not include the word "stupid"! I am truly sorry
if it came over as offensive. Let's end this discussion as it does not
have much to do with GROMACS anymore.
good luck with your topology
warmest regards
Daan
On Tue, 15 Jun 2004, Semen Esilevsky wrote:
> 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
> ============
>
>
>
>
>
>
> __________________________________
> Do you Yahoo!?
> Yahoo! Mail - Helps protect you from nasty viruses.
> http://promotions.yahoo.com/new_mail
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
##############################################################################
Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
School of Life Sciences E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk
More information about the gromacs.org_gmx-users
mailing list