From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Jan 24 2010 - 14:18:22 CST

Ronald,
  If you're interested in writing such a plugin, I would expect
that you could still use the lower-level psfgen plugin to do all
of the structure assembly tasks and file output for you, so you
shouldn't even need to write a PSF file directly from your own
code. Unfortunately, there's not much documentation on the PSF
format, and there are different minor variations associated with
Charmm, X-PLOR, and NAMD, so it is quite difficult to get it right.
I would suggest having the psfgen plugin do the leg work for you, and
have it emit the actual PSF files using the existing VMD molfile plugins
and its own PSF code. If you are desperate, you can read the VMD
psfplugin source code, but again, I'd instead recommand having psfgen
do this for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jan 24, 2010 at 02:09:57PM -0600, Ronald Salesky wrote:
> 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
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078