[Dock-fans] problem with dms:

Parminder Mankoo pkmankoo at gmail.com
Tue Jul 24 16:08:22 PDT 2007


Hello,

I am trying to learn DOCK6 to dock atp into a kinase. I am following the
tutorials and now stuck at the step where I need
_____________________
../dms/bin/dms atp.pdb -n -w 1.4 -v -o atp.ms

No atoms in input file!
________________________

The atp.pdb file is not empty. It is as following:

I will appreciate any help.
Thanks, preeti

EXPDTA    THEORETICAL MODEL, MODELLER SVN 2007/07/16 21:23:51
ATOM      1  PG  ATP  1391      28.876  68.006  19.624  1.00 92.35
P
ATOM      2  O3B ATP  1391      27.839  66.717  19.158  1.00 91.75
O
ATOM      3  PB  ATP  1391      27.136  66.147  17.708  1.00 89.86
P
ATOM      4  O3A ATP  1391      25.700  65.646  18.125  1.00 89.34
O
ATOM      5  PA  ATP  1391      24.999  64.238  18.558  1.00 88.85
P
ATOM      6  O5' ATP  1391      23.527  64.665  18.713  1.00 86.03
O
ATOM      7  C5' ATP  1391      23.084  65.460  19.796  1.00 84.42
C
ATOM      8  C4' ATP  1391      21.636  65.673  19.598  1.00 80.99
C
ATOM      9  C3' ATP  1391      20.999  66.481  20.692  1.00 80.39
C
ATOM     10  C2' ATP  1391      20.210  65.462  21.489  1.00 78.56
C
ATOM     11  C1' ATP  1391      20.120  64.139  20.656  1.00 76.25
C
ATOM     12  N9  ATP  1391      20.605  62.931  21.426  1.00 72.25
N
ATOM     13  C4  ATP  1391      19.867  62.159  22.282  1.00 69.34
C
ATOM     14  N3  ATP  1391      18.539  62.305  22.599  1.00 67.00
N
ATOM     15  C2  ATP  1391      18.146  61.357  23.483  1.00 66.09
C
ATOM     16  N1  ATP  1391      18.880  60.379  24.016  1.00 66.25
N
ATOM     17  C6  ATP  1391      20.194  60.265  23.667  1.00 67.23
C
ATOM     18  N6  ATP  1391      20.953  59.309  24.176  1.00 66.15
N
ATOM     19  C5  ATP  1391      20.737  61.194  22.759  1.00 69.38
C
ATOM     20  N7  ATP  1391      22.010  61.321  22.230  1.00 70.26
N
ATOM     21  C8  ATP  1391      21.872  62.362  21.456  1.00 70.59
C
ATOM     22  O4' ATP  1391      21.008  64.371  19.546  1.00 79.07
O
ATOM     23  O2' ATP  1391      18.893  65.918  21.763  1.00 79.22
O
ATOM     24  O3' ATP  1391      20.174  67.484  20.024  1.00 83.82
O
ATOM     25  O2A ATP  1391      25.487  63.690  19.829  1.00 86.17
O
ATOM     26  O1A ATP  1391      25.072  63.410  17.343  1.00 90.83
O
ATOM     27  O2B ATP  1391      27.063  67.238  16.699  1.00 92.00
O
ATOM     28  O1B ATP  1391      27.841  64.910  17.278  1.00 89.89
O
ATOM     29  O3G ATP  1391      28.367  68.556  20.926  1.00 91.62
O
ATOM     30  O2G ATP  1391      30.180  67.348  19.772  1.00 93.97
O
ATOM     31  O1G ATP  1391      28.827  69.027  18.566  1.00 93.43
O
END
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