VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 17 2006 - 09:57:46 CST

Hi Lavina,
XBGF is an internal format used by some vmd plugins; it is based on the
MSI biograf format, but has some extensions. Could you tell me what
version of the beta you are running? And is this on windows? There was a
windows bug that caused this behavior (failure to delete a temp file)
that should be fixed in the latest version of the beta. If it is not
please let me know, and I will double check our source and send you an
updated version of the plugin.
Best,
Peter

Lin wrote:

>hi, i used the autopsf plugin in VMD 1.84b, and it failed
>coz it says it cant delete the pdb file as permission is
>denied. and i got 3 output files, .XBGF, .TOP and .PDB.
>as attached. may i know what is the reason? Also, wat is
>a .XBGF file?
>
>thanks a lot!
>
>regards,
>Lavina
>
>
>
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>------------------------------------------------------------------------
>
>ATOM 1 N ALA X 2 0.000 0.000 0.000 1.00 3.00 MAIN
>ATOM 2 H ALA X 2 -0.490 -0.462 -0.712 1.00 0.00 MAIN
>ATOM 3 CA ALA X 2 1.450 0.000 0.000 1.00 7.00 MAIN
>ATOM 4 CB ALA X 2 1.969 -0.670 -1.262 1.00 0.00 MAIN
>ATOM 5 C ALA X 2 2.010 1.413 0.000 1.00 0.00 MAIN
>ATOM 6 O ALA X 2 2.911 1.748 0.767 1.00 1.00 MAIN
>ATOM 7 N ALA X 3 1.488 2.280 -0.863 1.00 0.00 MAIN
>ATOM 8 H ALA X 3 0.770 1.998 -1.467 1.00 4.00 MAIN
>ATOM 9 CA ALA X 3 1.981 3.643 -0.909 1.00 7.00 MAIN
>ATOM 10 CB ALA X 3 1.147 4.464 -1.880 1.00 0.00 MAIN
>ATOM 11 C ALA X 3 1.865 4.326 0.444 1.00 0.00 MAIN
>ATOM 12 O ALA X 3 2.801 4.963 0.924 1.00 0.00 MAIN
>ATOM 13 N ALA X 4 0.710 4.211 1.093 1.00 9.00 MAIN
>ATOM 14 H ALA X 4 -0.026 3.700 0.697 1.00 0.00 MAIN
>ATOM 15 CA ALA X 4 0.541 4.841 2.388 1.00 7.00 MAIN
>ATOM 16 CB ALA X 4 -0.809 4.462 2.976 1.00 8.00 MAIN
>ATOM 17 C ALA X 4 1.591 4.371 3.381 1.00 0.00 MAIN
>ATOM 18 O ALA X 4 2.212 5.167 4.085 1.00 0.00 MAIN
>ATOM 19 N ALA X 5 1.818 3.063 3.463 1.00 0.00 MAIN
>ATOM 20 H ALA X 5 1.315 2.443 2.895 1.00 0.00 MAIN
>ATOM 21 CA ALA X 5 2.809 2.556 4.392 1.00 7.00 MAIN
>ATOM 22 CB ALA X 5 2.970 1.055 4.209 1.00 0.00 MAIN
>ATOM 23 C ALA X 5 4.176 3.170 4.142 1.00 0.00 MAIN
>ATOM 24 O ALA X 5 4.859 3.615 5.064 1.00 0.00 MAIN
>ATOM 25 N ALA X 6 4.611 3.212 2.886 1.00 0.00 MAIN
>ATOM 26 H ALA X 6 4.055 2.853 2.163 1.00 0.00 MAIN
>ATOM 27 CA ALA X 6 5.908 3.786 2.586 1.00 7.00 MAIN
>ATOM 28 CB ALA X 6 6.121 3.830 1.082 1.00 0.00 MAIN
>ATOM 29 C ALA X 6 6.012 5.221 3.079 1.00 0.00 MAIN
>ATOM 30 O ALA X 6 6.992 5.614 3.710 1.00 0.00 MAIN
>ATOM 31 N ALA X 7 5.002 6.040 2.802 1.00 0.00 MAIN
>ATOM 32 H ALA X 7 4.228 5.711 2.297 1.00 0.00 MAIN
>ATOM 33 CA ALA X 7 5.044 7.419 3.245 1.00 7.00 MAIN
>ATOM 34 CB ALA X 7 3.730 8.110 2.918 1.00 0.00 MAIN
>ATOM 35 C ALA X 7 5.219 7.518 4.752 1.00 0.00 MAIN
>ATOM 36 O ALA X 7 6.045 8.278 5.255 1.00 0.00 MAIN
>ATOM 37 N ALA X 8 4.445 6.748 5.512 1.00 0.00 MAIN
>ATOM 38 H ALA X 8 3.792 6.148 5.096 1.00 0.00 MAIN
>ATOM 39 CA ALA X 8 4.566 6.799 6.956 1.00 7.00 MAIN
>ATOM 40 CB ALA X 8 3.670 5.747 7.589 1.00 0.00 MAIN
>ATOM 41 C ALA X 8 5.984 6.488 7.409 1.00 0.00 MAIN
>ATOM 42 O ALA X 8 6.560 7.186 8.241 1.00 0.00 MAIN
>ATOM 43 N ALA X 9 6.582 5.429 6.871 1.00 0.00 MAIN
>ATOM 44 H ALA X 9 6.109 4.882 6.209 1.00 0.00 MAIN
>ATOM 45 CA ALA X 9 7.934 5.082 7.264 1.00 7.00 MAIN
>ATOM 46 CB ALA X 9 8.436 3.918 6.425 1.00 0.00 MAIN
>ATOM 47 C ALA X 9 8.898 6.233 7.027 1.00 0.00 MAIN
>ATOM 48 O ALA X 9 9.705 6.584 7.887 1.00 0.00 MAIN
>ATOM 49 N ALA X 10 8.839 6.851 5.851 1.00 0.00 MAIN
>ATOM 50 H ALA X 10 8.190 6.560 5.176 1.00 0.00 MAIN
>ATOM 51 CA ALA X 10 9.733 7.956 5.567 1.00 7.00 MAIN
>ATOM 52 CB ALA X 10 9.388 8.570 4.219 1.00 0.00 MAIN
>ATOM 53 C ALA X 10 9.595 9.067 6.595 1.00 0.00 MAIN
>ATOM 54 O ALA X 10 10.580 9.587 7.117 1.00 0.00 MAIN
>ATOM 55 N ALA X 11 8.364 9.460 6.912 1.00 0.00 MAIN
>ATOM 56 H ALA X 11 7.590 9.036 6.488 1.00 0.00 MAIN
>ATOM 57 CA ALA X 11 8.169 10.516 7.887 1.00 7.00 MAIN
>ATOM 58 CB ALA X 11 6.686 10.695 8.168 1.00 0.00 MAIN
>ATOM 59 C ALA X 11 8.823 10.177 9.217 1.00 0.00 MAIN
>ATOM 60 O ALA X 11 9.523 10.992 9.815 1.00 0.00 MAIN
>
>