ADL: strange error in autodock4 output

snoze pa snoze.pa at gmail.com
Mon Mar 3 07:54:47 PST 2008


Please read my previous mail as:

'Cl' atom is present in both *gpf *and *dpf* files but in *dlg* file it is
showing only 'l' not 'Cl' atom.
Any idea?



On Mon, Mar 3, 2008 at 9:48 AM, snoze pa <snoze.pa at gmail.com> wrote:

> Dear Autodock users,
>  I am getting strange error in audock4 calculation. I am using following
> ligand in my calculation and all dlg and dpf files are showing the atom
> 'Cl'
> properly. But when I run autodock4 it only print 'l' not 'Cl' in output
> dock.dlg file. I am also showing one output from the autodock4
> calculation.
> I will higly appreciate your help.
>
> input ligand:
>
> ATOM      1  C           0      -0.526   0.552   0.079  0.00  0.00
> C+0
> ATOM      2  C           0      -2.356  -1.020   0.096  0.00  0.00
> C+0
> ATOM      3  C           0      -0.991  -0.771   0.091  0.00  0.00
> C+0
> ATOM      4  C           0       0.918   0.828   0.073  0.00  0.00
> C+0
> ATOM      5  C           0      -3.252   0.032   0.080  0.00  0.00
> C+0
> ATOM      6  C           0       5.835   0.618   0.060  0.00  0.00
> C+0
> ATOM      7  C           0      -1.444   1.608   0.068  0.00  0.00
> C+0
> ATOM      8  C           0      -2.797   1.342   0.068  0.00  0.00
> C+0
> ATOM      9  C           0       5.355  -0.527   0.670  0.00  0.00
> C+0
> ATOM     10  C           0       3.115   0.099   0.072  0.00  0.00
> C+0
> ATOM     11  C           0       4.961   1.506  -0.545  0.00  0.00
> C+0
> ATOM     12  C           0       0.154  -2.128  -1.270  0.00  0.00
> C+0
> ATOM     13  C           0       4.002  -0.792   0.680  0.00  0.00
> C+0
> ATOM     14  C           0       3.606   1.253  -0.542  0.00  0.00
> C+0
> ATOM     15  O           0      -0.110  -1.804   0.096  0.00  0.00
> O+0
> ATOM     16 Cl           0      -3.935   2.652   0.047  0.00  0.00
> Cl+0
> ATOM     17 Cl           0      -2.939  -2.655   0.110  0.00  0.00
> Cl+0
> ATOM     18  N           0       1.770  -0.158   0.078  0.00  0.00
> N+0
> ATOM     19  H           0       1.273   1.848   0.064  0.00  0.00
> H+0
> ATOM     20  H           0      -4.314  -0.167   0.079  0.00  0.00
> H+0
> ATOM     21  H           0       6.895   0.823   0.059  0.00  0.00
> H+0
> ATOM     22  H           0      -1.094   2.629   0.059  0.00  0.00
> H+0
> ATOM     23  H           0       6.043  -1.215   1.140  0.00  0.00
> H+0
> ATOM     24  H           0       5.342   2.398  -1.019  0.00  0.00
> H+0
> ATOM     25  H           0       0.861  -2.957  -1.316  0.00  0.00
> H+0
> ATOM     26  H           0      -0.775  -2.415  -1.762  0.00  0.00
> H+0
> ATOM     27  H           0       0.579  -1.260  -1.774  0.00  0.00
> H+0
> ATOM     28  H           0       3.629  -1.687   1.157  0.00  0.00
> H+0
> ATOM     29  H           0       2.925   1.946  -1.015  0.00  0.00
> H+0
> CONECT    1    3    4    7    0
> NONE  34
> CONECT    2    3   17    5    0
> NONE  35
> CONECT    3    2    1   15    0
> NONE  36
> CONECT    4    1   18   19    0
> NONE  37
> CONECT    5    8    2   20    0
> NONE  38
> CONECT    6   11    9   21    0
> NONE  39
> CONECT    7    1    8   22    0
> NONE  40
> CONECT    8    5    7   16    0
> NONE  41
> CONECT    9   13    6   23    0
> NONE  42
> CONECT   10   18   13   14    0
> NONE  43
> CONECT   11   14    6   24    0
> NONE  44
> CONECT   12   15   25   26   27
> NONE  45
> CONECT   13   10    9   28    0
> NONE  46
> CONECT   14   10   11   29    0
> NONE  47
> CONECT   15    3   12    0    0
> NONE  48
> CONECT   16    8    0    0    0
> NONE  49
> CONECT   17    2    0    0    0
> NONE  50
> CONECT   18    4   10    0    0
> NONE  51
> END
>
>
>
> Docked ligand in .dlg file
>
> ATOM      1  C           0      30.813  42.933  41.866 -0.39 +0.01
>  +0.018
> 64.691
> ATOM      2  C           0      32.010  45.025  41.750 -0.29 +0.02
>  +0.069
> 64.691
> ATOM      3  C           0      31.011  44.188  41.272 -0.26 +0.08
>  +0.101
> 64.691
> ATOM      4  C           0      32.810  44.618  42.801 -0.39 +0.01
>  +0.050
> 64.691
> ATOM      5  C           0      31.627  42.536  42.933 -0.39 +0.01
>  +0.039
> 64.691
> ATOM      6  C           0      32.618  43.378  43.391 -0.43 +0.01
>  +0.036
> 64.691
> ATOM      7  l           0      33.632  42.882  44.709 -0.74 -0.00    -
> 0.084
> 64.691
> ATOM      8  l           0      32.262  46.579  41.019 -0.42 -0.01    -
> 0.081
> 64.691
> ATOM      9  C           0      29.758  42.038  41.368 -0.38 +0.13
>  +0.131
> 64.691
> ATOM     10  N           0      29.508  40.918  41.985 -0.35 -0.18    -
> 0.260
> 64.691
> ATOM     11  C           0      28.526  40.085  41.522 -0.50 +0.04
>  +0.056
> 64.691
> ATOM     12  C           0      27.426  40.609  40.840 -0.39 +0.02
>  +0.031
> 64.691
> ATOM     13  C           0      26.440  39.764  40.375 -0.40 +0.00
>  +0.002
> 64.691
> ATOM     14  C           0      26.539  38.400  40.583 -0.35 +0.00
>  +0.000
> 64.691
> ATOM     15  C           0      27.628  37.873  41.259 -0.60 +0.00
>  +0.002
> 64.691
> ATOM     16  C           0      28.620  38.707  41.728 -0.43 +0.01
>  +0.031
> 64.691
> ATOM     17  O           0      30.231  44.583  40.233 -0.61 -0.47    -
> 0.353
> 64.691
> ATOM     18  C           0      29.103  45.254  40.796 -0.17 +0.13
>  +0.210
> 64.691
> TER
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