VMD-L Mailing List

From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Sun Jan 24 2010 - 14:09:57 CST

Hello Peter and John,

Thank you for your suggestions! The atoms are "Amber99"
atoms as generated by Tinker. It's been quite an adventure
going from a program that will generate a nucleic acid
sequence to VMD. Namot results in very strange
connectivity as does Tinker and I suspect it is the atom
naming conventions as you point out. A nucleic acid
generator plugin would be very cool for VMD! (once
ascending these learning curves, I hope to write one and
make some small contribution)

Is there a .psf format reference? The only thing I could
find was a comment from circa 1999 that it had been
"reverse engineered" by looking at X-plor output by one of
the developers of NAMD.

Best regards,

Ron

On Sun, 24 Jan 2010 14:55:07 -0500
  Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Ronald,
> my first suggestion is to try going through the steps of
>autopsf
> (described in the documentation) instead of using the
>I'm feeling lucky
> button, which is really just designed to make the most
>common use case
> (small globular proteins with recognizable ligands)
>easy. For anything
> that it doesn't work well for, stepping through the gui
>is the way to
> go, and following all of the steps is in fact the
>primary intended mode
> of usage of the plugin.
>
> Also, you definitely need to re-name all of your atoms
>to match the
> names in the topology file; otherwise psfgen has no way
>of knowing which
> of your atoms match up with which atoms in the
>structure, and you'll get
> the exceedingly odd bonding pattern that John described.
>
> Best,
> Peter
>
> Ronald Salesky wrote:
>> Hello fellow VMD users,
>>
>> I am attempting to generate a psf file using the Autopsf
>>plugin
>> utility from a loaded .pdb molecule. The molecule is
>>displayed
>> beautifully in the VMD viewer and 129 atoms are listed
>>in VMD main as
>> the number of atoms, yet autopsf gives the error, "Need
>>to have at
>> least one atom in your selection!". Does anyone have a
>>suggestion?
>> I've used this plugin before with other .pdb files w/o
>>encountering
>> this error (and not doing anything special other than
>>launching
>> autopsf and pressing "I'm feeling lucky".)
>>
>> I have attached the .pdb in question as background.
>>Please note that
>> this .pdb represents a ssDNA strand AGCT which was
>>generated w/
>> Tinker's nucleic and the .pdb generated from the VegaZZ
>>program by
>> opening the Tinker .xyz file and outputting the .pdb
>>file. (I then
>> filled in the residue name, chainID and residue sequence
>>numbers by
>> hand in the columns indicated by the .pdb format
>>definition as VegaZZ
>> had listed the res as UNK, w/ 1 seq number for the whole
>>chain and no
>> chainID)
>>
>> Much thanks in advance,
>>
>> Ron
>>
>> PS: Additionally, other than the psfgen user's manual,
>>can anyone
>> point me to a good tutorial on psfgen and a format
>>definition for .psf
>> files?
>>
>> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P
>>1 1
>> ATOM 1 OH ADE A 1 0.000 0.000 0.000
>>1.00 0.00
>> ATOM 2 CT ADE A 1 0.000 0.000 1.440
>>1.00 0.00
>> ATOM 3 CT ADE A 1 1.427 0.000 1.962
>>1.00 0.00
>> ATOM 4 OS ADE A 1 1.924 -1.373 1.980
>>1.00 0.00
>> ATOM 5 CT ADE A 1 2.867 -1.557 0.934
>>1.00 0.00
>> ATOM 6 CT ADE A 1 2.436 0.817 1.152
>>1.00 0.00
>> ATOM 7 CT ADE A 1 2.833 -0.159 0.042
>>1.00 0.00
>> ATOM 8 OS ADE A 1 3.554 1.211 1.932
>>1.00 0.00
>> ATOM 9 OH ADE A 1 4.152 0.148 -0.414
>>1.00 0.00
>> ATOM 10 HO ADE A 1 -0.918 0.000 -0.281
>>1.00 0.00
>> ATOM 11 H1 ADE A 1 -0.521 -0.886 1.804
>>1.00 0.00
>> ATOM 12 H1 ADE A 1 -0.521 0.886 1.804
>>1.00 0.00
>> ATOM 13 H1 ADE A 1 1.436 0.337 2.999
>>1.00 0.00
>> ATOM 14 H2 ADE A 1 3.838 -1.808 1.360
>>1.00 0.00
>> ATOM 15 H1 ADE A 1 1.936 1.681 0.714
>>1.00 0.00
>> ATOM 16 H1 ADE A 1 2.032 -0.217 -0.695
>>1.00 0.00
>> ATOM 17 HO ADE A 1 4.364 -0.482 -1.106
>>1.00 0.00
>> ATOM 18 N* ADE A 1 2.474 -2.761 0.168
>>1.00 0.00
>> ATOM 19 CK ADE A 1 1.538 -2.869 -0.826
>>1.00 0.00
>> ATOM 20 NB ADE A 1 1.421 -4.071 -1.308
>>1.00 0.00
>> ATOM 21 CB ADE A 1 2.345 -4.815 -0.583
>>1.00 0.00
>> ATOM 22 CA ADE A 1 2.705 -6.168 -0.620
>>1.00 0.00
>> ATOM 23 N2 ADE A 1 2.152 -7.058 -1.455
>>1.00 0.00
>> ATOM 24 NC ADE A 1 3.661 -6.580 0.240
>>1.00 0.00
>> ATOM 25 CQ ADE A 1 4.205 -5.691 1.066
>>1.00 0.00
>> ATOM 26 NC ADE A 1 3.950 -4.402 1.192
>>1.00 0.00
>> ATOM 27 CB ADE A 1 2.992 -4.015 0.323
>>1.00 0.00
>> ATOM 28 H5 ADE A 1 0.952 -2.033 -1.178
>>1.00 0.00
>> ATOM 29 H ADE A 1 2.449 -8.012 -1.437
>>1.00 0.00
>> ATOM 30 H ADE A 1 1.443 -6.767 -2.097
>>1.00 0.00
>> ATOM 31 H5 ADE A 1 4.964 -6.080 1.730
>>1.00 0.00
>> ATOM 32 P GUA A 2 4.945 1.510 1.200
>>1.00 0.00
>> ATOM 33 O2 GUA A 2 4.678 1.881 -0.208
>>1.00 0.00
>> ATOM 34 O2 GUA A 2 5.626 2.625 1.895
>>1.00 0.00
>> ATOM 35 OS GUA A 2 5.703 0.109 1.353
>>1.00 0.00
>> ATOM 36 CT GUA A 2 5.700 -0.549 2.634
>>1.00 0.00
>> ATOM 37 CT GUA A 2 7.006 -1.298 2.839
>>1.00 0.00
>> ATOM 38 OS GUA A 2 6.912 -2.602 2.189
>>1.00 0.00
>> ATOM 39 CT GUA A 2 7.704 -2.610 1.010
>>1.00 0.00
>> ATOM 40 CT GUA A 2 8.259 -0.622 2.279
>>1.00 0.00
>> ATOM 41 CT GUA A 2 8.235 -1.051 0.810
>>1.00 0.00
>> ATOM 42 OS GUA A 2 9.441 -1.058 2.936
>>1.00 0.00
>> ATOM 43 OH GUA A 2 9.568 -1.064 0.294
>>1.00 0.00
>> ATOM 44 H1 GUA A 2 4.867 -1.251 2.680
>>1.00 0.00
>> ATOM 45 H1 GUA A 2 5.577 0.191 3.424
>>1.00 0.00
>> ATOM 46 H1 GUA A 2 7.147 -1.501 3.901
>>1.00 0.00
>> ATOM 47 H2 GUA A 2 8.493 -3.356 1.107
>>1.00 0.00
>> ATOM 48 H1 GUA A 2 8.149 0.460 2.344
>>1.00 0.00
>> ATOM 49 H1 GUA A 2 7.479 -0.475 0.276
>>1.00 0.00
>> ATOM 50 HO GUA A 2 9.511 -1.336 -0.625
>>1.00 0.00
>> ATOM 51 N* GUA A 2 6.864 -3.100 -0.105
>>1.00 0.00
>> ATOM 52 CK GUA A 2 5.959 -2.394 -0.871
>>1.00 0.00
>> ATOM 53 NB GUA A 2 5.364 -3.112 -1.791
>>1.00 0.00
>> ATOM 54 CB GUA A 2 5.910 -4.380 -1.626
>>1.00 0.00
>> ATOM 55 C GUA A 2 5.661 -5.567 -2.325
>>1.00 0.00
>> ATOM 56 O GUA A 2 4.888 -5.762 -3.261
>>1.00 0.00
>> ATOM 57 NA GUA A 2 6.435 -6.623 -1.830
>>1.00 0.00
>> ATOM 58 CA GUA A 2 7.335 -6.530 -0.788
>>1.00 0.00
>> ATOM 59 N2 GUA A 2 7.980 -7.658 -0.463
>>1.00 0.00
>> ATOM 60 NC GUA A 2 7.570 -5.401 -0.125
>>1.00 0.00
>> ATOM 61 CB GUA A 2 6.826 -4.363 -0.593
>>1.00 0.00
>> ATOM 62 H5 GUA A 2 5.758 -1.342 -0.725
>>1.00 0.00
>> ATOM 63 H GUA A 2 6.327 -7.516 -2.266
>>1.00 0.00
>> ATOM 64 H GUA A 2 7.796 -8.502 -0.967
>>1.00 0.00
>> ATOM 65 H GUA A 2 8.645 -7.657 0.283
>>1.00 0.00
>> ATOM 66 P CYT A 3 10.836 -0.976 2.157
>>1.00 0.00
>> ATOM 67 O2 CYT A 3 10.743 0.065 1.110
>>1.00 0.00
>> ATOM 68 O2 CYT A 3 11.905 -0.630 3.120
>>1.00 0.00
>> ATOM 69 OS CYT A 3 10.969 -2.458 1.568
>>1.00 0.00
>> ATOM 70 CT CYT A 3 10.699 -3.579 2.431
>>1.00 0.00
>> ATOM 71 CT CYT A 3 11.596 -4.749 2.062
>>1.00 0.00
>> ATOM 72 OS CYT A 3 10.989 -5.480 0.953
>>1.00 0.00
>> ATOM 73 CT CYT A 3 11.714 -5.230 -0.242
>>1.00 0.00
>> ATOM 74 CT CYT A 3 13.016 -4.390 1.620
>>1.00 0.00
>> ATOM 75 CT CYT A 3 12.825 -4.059 0.139
>>1.00 0.00
>> ATOM 76 OS CYT A 3 13.923 -5.467 1.807
>>1.00 0.00
>> ATOM 77 OH CYT A 3 14.043 -4.309 -0.567
>>1.00 0.00
>> ATOM 78 H1 CYT A 3 9.655 -3.874 2.328
>>1.00 0.00
>> ATOM 79 H1 CYT A 3 10.882 -3.293 3.467
>>1.00 0.00
>> ATOM 80 H1 CYT A 3 11.641 -5.450 2.896
>>1.00 0.00
>> ATOM 81 H2 CYT A 3 12.137 -6.163 -0.612
>>1.00 0.00
>> ATOM 82 H1 CYT A 3 13.348 -3.499 2.152
>>1.00 0.00
>> ATOM 83 H1 CYT A 3 12.365 -3.075 0.042
>>1.00 0.00
>> ATOM 84 HO CYT A 3 13.884 -4.090 -1.488
>>1.00 0.00
>> ATOM 85 N* CYT A 3 10.750 -4.818 -1.287
>>1.00 0.00
>> ATOM 86 C CYT A 3 10.319 -5.773 -2.170
>>1.00 0.00
>> ATOM 87 O CYT A 3 10.750 -6.931 -2.058
>>1.00 0.00
>> ATOM 88 NC CYT A 3 9.420 -5.410 -3.152
>>1.00 0.00
>> ATOM 89 CA CYT A 3 8.979 -4.148 -3.240
>>1.00 0.00
>> ATOM 90 N2 CYT A 3 8.120 -3.850 -4.197
>>1.00 0.00
>> ATOM 91 CM CYT A 3 9.416 -3.136 -2.328
>>1.00 0.00
>> ATOM 92 CM CYT A 3 10.302 -3.514 -1.368
>>1.00 0.00
>> ATOM 93 H CYT A 3 7.815 -4.559 -4.833
>>1.00 0.00
>> ATOM 94 H CYT A 3 7.774 -2.916 -4.285
>>1.00 0.00
>> ATOM 95 HA CYT A 3 9.060 -2.119 -2.399
>>1.00 0.00
>> ATOM 96 H4 CYT A 3 10.660 -2.784 -0.658
>>1.00 0.00
>> ATOM 97 P THY A 4 15.236 -5.543 0.896
>>1.00 0.00
>> ATOM 98 O2 THY A 4 15.570 -4.183 0.419
>>1.00 0.00
>> ATOM 99 O2 THY A 4 16.352 -6.083 1.704
>>1.00 0.00
>> ATOM 100 OS THY A 4 14.765 -6.528 -0.274
>>1.00 0.00
>> ATOM 101 CT THY A 4 14.067 -7.739 0.071
>>1.00 0.00
>> ATOM 102 CT THY A 4 14.421 -8.844 -0.911
>>1.00 0.00
>> ATOM 103 OS THY A 4 13.574 -8.714 -2.093
>>1.00 0.00
>> ATOM 104 CT THY A 4 14.342 -8.223 -3.183
>>1.00 0.00
>> ATOM 105 CT THY A 4 15.867 -8.856 -1.411
>>1.00 0.00
>> ATOM 106 CT THY A 4 15.828 -7.840 -2.554
>>1.00 0.00
>> ATOM 107 OH THY A 4 16.265 -10.142 -1.861
>>1.00 0.00
>> ATOM 108 H1 THY A 4 12.992 -7.559 0.045
>>1.00 0.00
>> ATOM 109 H1 THY A 4 14.346 -8.045 1.079
>>1.00 0.00
>> ATOM 110 H1 THY A 4 14.179 -9.812 -0.472
>>1.00 0.00
>> ATOM 111 H2 THY A 4 14.356 -8.965 -3.981
>>1.00 0.00
>> ATOM 112 H1 THY A 4 16.527 -8.492 -0.623
>>1.00 0.00
>> ATOM 113 HC THY A 4 15.800 -6.831 -2.143
>>1.00 0.00
>> ATOM 114 HC THY A 4 16.603 -8.081 -3.281
>>1.00 0.00
>> ATOM 115 HO THY A 4 17.168 -10.197 -2.184
>>1.00 0.00
>> ATOM 116 N* THY A 4 13.626 -7.066 -3.765
>>1.00 0.00
>> ATOM 117 C THY A 4 12.854 -7.301 -4.872
>>1.00 0.00
>> ATOM 118 O THY A 4 12.743 -8.406 -5.379
>>1.00 0.00
>> ATOM 119 NA THY A 4 12.203 -6.199 -5.386
>>1.00 0.00
>> ATOM 120 C THY A 4 12.260 -4.911 -4.892
>>1.00 0.00
>> ATOM 121 O THY A 4 11.632 -4.005 -5.438
>>1.00 0.00
>> ATOM 122 CM THY A 4 13.095 -4.763 -3.728
>>1.00 0.00
>> ATOM 123 CT THY A 4 13.211 -3.393 -3.129
>>1.00 0.00
>> ATOM 124 CM THY A 4 13.739 -5.817 -3.208
>>1.00 0.00
>> ATOM 125 H THY A 4 11.634 -6.347 -6.194
>>1.00 0.00
>> ATOM 126 HC THY A 4 12.609 -2.691 -3.706
>>1.00 0.00
>> ATOM 127 HC THY A 4 14.254 -3.077 -3.144
>>1.00 0.00
>> ATOM 128 HC THY A 4 12.856 -3.416 -2.099
>>1.00 0.00
>> ATOM 129 H4 THY A 4 14.359 -5.680 -2.335
>>1.00 0.00
>>
>> CONECT 1 2 10 2 10
>> CONECT 2 1 1 3 11
>> CONECT 2 12 3
>> CONECT 3 2 2 4 6
>> CONECT 3 13 4
>> CONECT 4 3 3 5 5
>> CONECT 5 4 4 7 14
>> CONECT 5 18 7
>> CONECT 6 3 7 8 15
>> CONECT 6 7 8
>> CONECT 7 5 6 5 6
>> CONECT 7 9 16
>> CONECT 8 6 6 32 32
>> CONECT 9 7 17 17
>> CONECT 10 1 1
>> CONECT 11 2
>> CONECT 12 2
>> CONECT 13 3
>> CONECT 14 5
>> CONECT 15 6
>> CONECT 16 7
>> CONECT 17 9 9
>> CONECT 18 5 19 27 19
>> CONECT 18 27
>> CONECT 19 18 18 20 28
>> CONECT 19 20 28
>> CONECT 20 19 19 21 21
>> CONECT 21 20 20 22 27
>> CONECT 21 22 27
>> CONECT 22 21 21 23 24
>> CONECT 22 23 24
>> CONECT 23 22 22 29 30
>> CONECT 23 29 30
>> CONECT 24 22 22 25 25
>> CONECT 25 24 24 26 31
>> CONECT 25 26 31
>> CONECT 26 25 25 27 27
>> CONECT 27 18 21 26 18
>> CONECT 27 21 26
>> CONECT 28 19 19
>> CONECT 29 23 23
>> CONECT 30 23 23
>> CONECT 31 25 25
>> CONECT 32 8 8 33 34
>> CONECT 32 35 33
>> CONECT 33 32 32
>> CONECT 34 32
>> CONECT 35 32 36 36
>> CONECT 36 35 35 37 44
>> CONECT 36 45 37
>> CONECT 37 36 36 38 40
>> CONECT 37 46 38
>> CONECT 38 37 37 39 39
>> CONECT 39 38 38 41 47
>> CONECT 39 51 41
>> CONECT 40 37 41 42 48
>> CONECT 40 41 42
>> CONECT 41 39 40 39 40
>> CONECT 41 43 49
>> CONECT 42 40 40 66 66
>> CONECT 43 41 50 50
>> CONECT 44 36
>> CONECT 45 36
>> CONECT 46 37
>> CONECT 47 39
>> CONECT 48 40
>> CONECT 49 41
>> CONECT 50 43 43
>> CONECT 51 39 52 61 52
>> CONECT 51 61
>> CONECT 52 51 51 53 62
>> CONECT 52 53 62
>> CONECT 53 52 52 54 54
>> CONECT 54 53 53 55 61
>> CONECT 54 55 61
>> CONECT 55 54 54 56 57
>> CONECT 55 56 57
>> CONECT 56 55 55
>> CONECT 57 55 55 58 63
>> CONECT 57 58 63
>> CONECT 58 57 57 59 60
>> CONECT 58 59 60
>> CONECT 59 58 58 64 65
>> CONECT 59 64 65
>> CONECT 60 58 58 61 61
>> CONECT 61 51 54 60 51
>> CONECT 61 54 60
>> CONECT 62 52 52
>> CONECT 63 57 57
>> CONECT 64 59 59
>> CONECT 65 59 59
>> CONECT 66 42 42 67 68
>> CONECT 66 69 67
>> CONECT 67 66 66
>> CONECT 68 66
>> CONECT 69 66 70 70
>> CONECT 70 69 69 71 78
>> CONECT 70 79 71
>> CONECT 71 70 70 72 74
>> CONECT 71 80 72
>> CONECT 72 71 71 73 73
>> CONECT 73 72 72 75 81
>> CONECT 73 85 75
>> CONECT 74 71 75 76 82
>> CONECT 74 75 76
>> CONECT 75 73 74 73 74
>> CONECT 75 77 83
>> CONECT 76 74 74 97 97
>> CONECT 77 75 84 84
>> CONECT 78 70
>> CONECT 79 70
>> CONECT 80 71
>> CONECT 81 73
>> CONECT 82 74
>> CONECT 83 75
>> CONECT 84 77 77
>> CONECT 85 73 86 92 86
>> CONECT 85 92
>> CONECT 86 85 85 87 88
>> CONECT 86 87 88
>> CONECT 87 86 86
>> CONECT 88 86 86 89 89
>> CONECT 89 88 88 90 91
>> CONECT 89 90 91
>> CONECT 90 89 89 93 94
>> CONECT 90 93 94
>> CONECT 91 89 89 92 95
>> CONECT 91 92 95
>> CONECT 92 85 91 85 91
>> CONECT 92 96 96
>> CONECT 93 90 90
>> CONECT 94 90 90
>> CONECT 95 91 91
>> CONECT 96 92 92
>> CONECT 97 76 76 98 99
>> CONECT 97 100 98
>> CONECT 98 97 97
>> CONECT 99 97
>> CONECT 100 97 101 101
>> CONECT 101 100 100 102 108
>> CONECT 101 109 102
>> CONECT 102 101 101 103 105
>> CONECT 102 110 103
>> CONECT 103 102 102 104 104
>> CONECT 104 103 103 106 111
>> CONECT 104 116 106
>> CONECT 105 102 106 107 112
>> CONECT 105 106 107
>> CONECT 106 104 105 104 105
>> CONECT 106 113 114
>> CONECT 107 105 105 115 115
>> CONECT 108 101
>> CONECT 109 101
>> CONECT 110 102
>> CONECT 111 104
>> CONECT 112 105
>> CONECT 113 106
>> CONECT 114 106
>> CONECT 115 107 107
>> CONECT 116 104 117 124 117
>> CONECT 116 124
>> CONECT 117 116 116 118 119
>> CONECT 117 118 119
>> CONECT 118 117 117
>> CONECT 119 117 117 120 125
>> CONECT 119 120 125
>> CONECT 120 119 119 121 122
>> CONECT 120 121 122
>> CONECT 121 120 120
>> CONECT 122 120 120 123 124
>> CONECT 122 123 124
>> CONECT 123 122 122 126 127
>> CONECT 123 128 126
>> CONECT 124 116 122 116 122
>> CONECT 124 129 129
>> CONECT 125 119 119
>> CONECT 126 123 123
>> CONECT 127 123
>> CONECT 128 123
>> CONECT 129 124 124
>>
>> END