ADL: Autodock distorting the molecule in docked pose

snoze pa snoze.pa at gmail.com
Fri Feb 29 08:06:03 PST 2008


Dear Autodock Users,


 I am trying to dock following compound(and similar other 100 more
compounds) to my protein. But in the dock pose autodock distort the
structure.  I don't know why, I can not open the docked pose in any pdb
viewer.

I can open the original compound below in any pdb viewer but not the docked
pose one.

Here is the original structure, the docked structure is also shown below

HETATM    1  C   UNK     1     -16.000   6.479   0.000  1.00  0.00
C
HETATM    2  C   UNK     1      -7.529   1.850   0.000  1.00  0.00
C
HETATM    3  C   UNK     1     -14.008   8.291   0.000  1.00  0.00
C
HETATM    4  C   UNK     1     -15.229   3.909   0.000  1.00  0.00
C
HETATM    5  C   UNK     1      10.729   1.988   0.000  1.00  0.00
C
HETATM    6  C   UNK     1       6.129  10.066   0.000  1.00  0.00
C
HETATM    7  C   UNK     1       6.341   4.704   0.000  1.00  0.00
C
HETATM    8  C   UNK     1       8.742   8.504   0.000  1.00  0.00
C
HETATM    9  C   UNK     1       6.237   2.134   0.000  1.00  0.00
C
HETATM   10  C   UNK     1       3.938   6.062   0.000  1.00  0.00
C
HETATM   11  C   UNK     1      -0.558   0.808   0.000  1.00  0.00
C
HETATM   12  C   UNK     1       1.667   2.204   0.000  1.00  0.00
C
HETATM   13  C   UNK     1       3.938   0.875   0.000  1.00  0.00
C
HETATM   14  C   UNK     1       1.667   4.775   0.000  1.00  0.00
C
HETATM   15  C   UNK     1     -10.729   4.979   0.000  1.00  0.00
C
HETATM   16  C   UNK     1     -12.716   3.208   0.000  1.00  0.00
C
HETATM   17  C   UNK     1     -11.392   7.562   0.000  1.00  0.00
C
HETATM   18  O   UNK     1       8.429   0.734   0.000  1.00  0.00
O
HETATM   19  O   UNK     1       3.866   8.713   0.000  1.00  0.00
O
HETATM   20  O   UNK     1       8.642   5.888   0.000  1.00  0.00
O
HETATM   21  N   UNK     1      -8.154   4.354   0.000  1.00  0.00
N
HETATM   22  N   UNK     1      -2.796   2.096   0.000  1.00  0.00
N
HETATM   23  N   UNK     1      -7.875  -2.404   0.000  1.00  0.00
N
HETATM   24  N   UNK     1      -9.238  -0.241   0.000  1.00  0.00
N
HETATM   25  N   UNK     1      -5.234  -1.812   0.000  1.00  0.00
N
HETATM   26  N   UNK     1      -5.021   0.808   0.000  1.00  0.00
N
CONECT    1    4    3
CONECT    2   26   24   21
CONECT    3   17    1
CONECT    4   16    1
CONECT    5   18
CONECT    6   19
CONECT    7   10   20    9
CONECT    8   20
CONECT    9   13   18    7
CONECT   10    7   14   19
CONECT   11   22   12
CONECT   12   11   13   14
CONECT   13    9   12
CONECT   14   10   12
CONECT   15   21   17   16
CONECT   16   15    4
CONECT   17   15    3
CONECT   18    9    5
CONECT   19   10    6
CONECT   20    7    8
CONECT   21    2   15
CONECT   22   26   11
CONECT   23   25   24
CONECT   24    2   23
CONECT   25   26   23
CONECT   26    2   25   22
MASTER        0    0    0    0    0    0    0    0   26    0   26    0
END



Here is the docked structure

ATOM      1  C   UNK     1      27.380  54.275  52.754 -0.22 +0.06    +0.150
80.947
ATOM      2  N   UNK     1      27.219  54.791  50.229 -0.21 -0.09    -0.176
80.947
ATOM      3  N   UNK     1      26.235  57.028  49.433 -0.18 -0.06    -0.124
80.947
ATOM      4  C   UNK     1      26.798  59.509  50.386 -0.04 +0.26    +0.280
80.947
ATOM      5  N   UNK     1      25.303  61.246  48.958 -0.43 -0.08    -0.120
80.947
ATOM      6  N   UNK     1      28.443  60.089  52.288 -0.32 -0.26    -0.213
80.947
ATOM      7  N   UNK     1      23.926  59.925  47.256 -0.64 +0.01    +0.021
80.947
ATOM      8  N   UNK     1      24.466  57.285  47.506 -0.52 -0.00    +0.021
80.947
ATOM      9  C   UNK     1      28.723  62.643  52.936 -0.08 +0.05    +0.062
80.947
ATOM     10  C   UNK     1      28.176  64.475  51.077 -0.18 +0.03    +0.046
80.947
ATOM     11  C   UNK     1      28.437  67.115  51.657 -0.26 +0.01    +0.011
80.947
ATOM     12  C   UNK     1      29.239  67.978  54.078 -0.27 +0.01    +0.026
80.947
ATOM     13  C   UNK     1      29.764  66.057  55.877 -0.16 -0.01    -0.025
80.947
ATOM     14  C   UNK     1      29.515  63.521  55.321 -0.05 +0.00    +0.010
80.947
ATOM     15  C   UNK     1      29.178  55.571  54.164 -0.11 +0.01    +0.039
80.947
ATOM     16  C   UNK     1      30.625  57.383  52.920 -0.14 +0.04    +0.056
80.947
ATOM     17  C   UNK     1      32.457  58.755  54.198 -0.12 +0.07    +0.096
80.947
ATOM     18  C   UNK     1      32.894  58.371  56.704 -0.12 +0.04    +0.130
80.947
ATOM     19  C   UNK     1      31.355  56.463  57.973 -0.18 +0.02    +0.096
80.947
ATOM     20  C   UNK     1      29.540  55.115  56.668 -0.25 +0.01    +0.056
80.947
ATOM     21  O   UNK     1      33.838  60.525  52.884 -0.44 -0.42    -0.330
80.947
ATOM     22  C   UNK     1      34.395  62.807  54.042 -0.17 +0.11    +0.181
80.947
ATOM     23  O   UNK     1      34.716  59.758  57.909 -0.13 -0.09    -0.325
80.947
ATOM     24  C   UNK     1      36.474  61.080  56.489 -0.26 +0.06    +0.182
80.947
ATOM     25  O   UNK     1      31.676  55.942  60.553 -0.11 -0.07    -0.330
80.947
ATOM     26  C   UNK     1      33.856  56.780  61.777 -0.13 +0.03    +0.181
80.947
TER


 I run 100 similar compounds and autodock is doing same to all compounds.
Any idea why i am not getting proper geometry
in my docked pose.

Thank you very much for your help.
s


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