VMD-L Mailing List

From: Ronald Salesky (rsalesky_at_unm.edu)
Date: Sun Jan 24 2010 - 12:43:51 CST

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