Subject: .dlg file in autodock

From: Ng Pei Ling <[email-masked]>
Date: Fri, 26 Apr 2002 00:33:16 -0700 (PDT)

To my friends : 

   For the attached file : 

  1.  Is the mean dock energy too high for enzyme 2hck dock with quercetin(ligand) ? The lowest dock energy is -6.77.

  2. What is the mean of 32 for the number of cluster ? It is mean there are 32 suitable conformation for docking? 

  3. What should I change in the input file to get lower docked energy? 

Thanks for yours help. 

Miss Ng Pei Ling
School of Pharmaceutical Sciences,

University Sciences Malaysia,

Minden 11800, Penang, Malaysia.

Tel:604-6577888 
Fax:604-6570017

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CLUSTERING HISTOGRAM 2HCK 
(Using UNIX Command Grep -i 'atom' 2hck1.pdbq > 2hck2.pdbq followed by 
 Grep -v 'REMARK' 2hck2.pdbq > 2hck3.pdbq)

________________________________________________________________________________
     |           |     |           |     |                                    
Clus | Lowest    | Run | Mean      | Num | Histogram                          
-ter | Docked    |     | Docked    | in  |                                    
Rank | Energy    |     | Energy    | Clus|    5    10   15   20   25   30   35
_____|___________|_____|___________|_____|____:____|____:____|____:____|____:___
   1 |     -6.88 |  32 |     -6.77 |   2 |##
   2 |     -6.48 |  34 |     -6.48 |   1 |#
   3 |     -5.97 |  99 |     -5.55 |  32 |################################
   4 |     -5.76 |  21 |     -5.76 |   1 |#
   5 |     -5.61 |  68 |     -5.61 |   1 |#
   6 |     -5.25 |   6 |     -5.25 |   1 |#
   7 |     -4.87 |  77 |     -4.80 |   2 |##
   8 |     -4.74 |  42 |     -4.73 |   2 |##
   9 |     -4.70 |  46 |     -4.70 |   1 |#
  10 |     -4.70 |  85 |     -4.70 |   1 |#
  11 |     -4.70 |  35 |     -4.55 |   4 |####
  12 |     -4.69 |  53 |     -4.69 |   1 |#
  13 |     -4.68 |  75 |     -4.68 |   1 |#
  14 |     -4.65 |  84 |     -4.65 |   1 |#
  15 |     -4.61 |   2 |     -4.61 |   1 |#
  16 |     -4.58 |  27 |     -4.49 |   6 |######
  17 |     -4.52 |  91 |     -4.47 |   2 |##
  18 |     -4.50 |  20 |     -4.50 |   2 |##
  19 |     -4.47 |  86 |     -4.46 |   2 |##
  20 |     -4.47 |  88 |     -4.47 |   1 |#
  21 |     -4.43 |  96 |     -4.37 |   5 |#####
  22 |     -4.42 |  36 |     -4.42 |   1 |#
  23 |     -4.42 |   1 |     -4.42 |   1 |#
  24 |     -4.39 |  10 |     -4.35 |   2 |##
  25 |     -4.38 |  57 |     -4.37 |   2 |##
  26 |     -4.36 |  38 |     -4.36 |   1 |#
  27 |     -4.35 |  56 |     -4.35 |   1 |#
  28 |     -4.32 |  47 |     -4.32 |   1 |#
  29 |     -4.30 |  79 |     -4.30 |   1 |#
  30 |     -4.27 |  14 |     -4.25 |   2 |##
  31 |     -4.27 |  64 |     -4.24 |   2 |##
  32 |     -4.23 |  18 |     -4.23 |   1 |#
  33 |     -4.19 |   8 |     -4.15 |   2 |##
  34 |     -4.18 |  61 |     -4.18 |   1 |#
  35 |     -4.16 |   9 |     -4.16 |   1 |#
  36 |     -4.16 |  58 |     -4.16 |   1 |#
  37 |     -4.15 |  70 |     -4.15 |   2 |##
  38 |     -4.14 |  65 |     -4.14 |   1 |#
  39 |     -4.09 |  19 |     -4.09 |   1 |#
  40 |     -3.96 |  82 |     -3.96 |   1 |#
  41 |     -3.90 | 100 |     -3.90 |   1 |#
  42 |     -3.85 |  28 |     -3.85 |   1 |#
  43 |     -3.77 |  63 |     -3.77 |   1 |#
  44 |     -3.72 |   4 |     -3.72 |   1 |#
  45 |     -2.04 |  87 |     -2.04 |   1 |#
_____|___________|_____|___________|_____|______________________________________

RMSD TABLE 2HCK

_____________________________________________________________________
     |      |      |           |         |                 |
Rank | Sub- | Run  | Docked    | Cluster | Reference       | Grep
     | Rank |      | Energy    | RMSD    | RMSD            | Pattern
_____|______|______|___________|_________|_________________|___________
   1      1     32       -6.88      0.00    137.36           RANKING
   1      2     29       -6.66      0.29    137.47           RANKING
   2      1     34       -6.48      0.00    137.57           RANKING
   3      1     99       -5.97      0.00    133.23           RANKING
   3      2     43       -5.97      0.05    133.21           RANKING
   3      3     31       -5.94      0.04    133.23           RANKING
   3      4     74       -5.90      0.09    133.20           RANKING
   3      5     52       -5.87      0.14    133.21           RANKING
   3      6     25       -5.87      0.18    133.19           RANKING
   3      7     30       -5.86      0.08    133.24           RANKING
   3      8     33       -5.85      0.13    133.19           RANKING
   3      9     78       -5.78      0.23    133.29           RANKING
   3     10     90       -5.76      0.21    133.29           RANKING
   3     11     92       -5.76      0.24    133.20           RANKING
   3     12     94       -5.70      0.18    133.25           RANKING
   3     13     16       -5.69      0.26    133.27           RANKING
   3     14     37       -5.66      0.29    133.20           RANKING
   3     15     67       -5.65      0.27    133.21           RANKING
   3     16     72       -5.64      0.32    133.34           RANKING
   3     17     98       -5.64      0.31    133.28           RANKING
   3     18     60       -5.60      0.35    133.35           RANKING
   3     19     69       -5.57      0.37    133.31           RANKING
   3     20     24       -5.56      0.33    133.35           RANKING
   3     21     54       -5.51      0.32    133.34           RANKING
   3     22     89       -5.43      0.33    133.31           RANKING
   3     23     83       -5.43      0.35    133.26           RANKING
   3     24     51       -5.39      0.39    133.30           RANKING
   3     25      5       -5.30      0.41    133.25           RANKING
   3     26     97       -5.24      0.28    133.14           RANKING
   3     27     15       -5.20      0.43    133.09           RANKING
   3     28     81       -5.16      0.50    133.30           RANKING
   3     29     62       -5.02      0.47    133.19           RANKING
   3     30     59       -4.99      0.45    133.08           RANKING
   3     31     66       -4.93      0.41    133.09           RANKING
   3     32     17       -4.87      0.47    133.08           RANKING
   4      1     21       -5.76      0.00    137.59           RANKING
   5      1     68       -5.61      0.00    133.86           RANKING
   6      1      6       -5.25      0.00    133.85           RANKING
   7      1     77       -4.87      0.00    132.82           RANKING
   7      2     50       -4.74      0.45    132.61           RANKING
   8      1     42       -4.74      0.00    131.30           RANKING
   8      2     80       -4.71      0.38    131.35           RANKING
   9      1     46       -4.70      0.00    133.09           RANKING
  10      1     85       -4.70      0.00    132.66           RANKING
  11      1     35       -4.70      0.00    133.31           RANKING
  11      2     11       -4.60      0.47    133.32           RANKING
  11      3      7       -4.56      0.49    133.32           RANKING
  11      4     39       -4.35      0.37    133.24           RANKING
  12      1     53       -4.69      0.00    131.72           RANKING
  13      1     75       -4.68      0.00    132.39           RANKING
  14      1     84       -4.65      0.00    131.85           RANKING
  15      1      2       -4.61      0.00    132.77           RANKING
  16      1     27       -4.58      0.00    130.90           RANKING
  16      2     73       -4.57      0.20    130.84           RANKING
  16      3     13       -4.56      0.44    131.08           RANKING
  16      4     40       -4.50      0.10    130.92           RANKING
  16      5     76       -4.39      0.26    130.81           RANKING
  16      6     12       -4.36      0.32    130.83           RANKING
  17      1     91       -4.52      0.00    132.58           RANKING
  17      2     23       -4.43      0.21    132.45           RANKING
  18      1     20       -4.50      0.00    138.07           RANKING
  18      2     55       -4.49      0.30    138.25           RANKING
  19      1     86       -4.47      0.00    133.21           RANKING
  19      2     26       -4.45      0.12    133.20           RANKING
  20      1     88       -4.47      0.00    133.23           RANKING
  21      1     96       -4.43      0.00    133.56           RANKING
  21      2     71       -4.40      0.22    133.47           RANKING
  21      3     22       -4.36      0.26    133.37           RANKING
  21      4     95       -4.34      0.46    133.35           RANKING
  21      5      3       -4.32      0.38    133.58           RANKING
  22      1     36       -4.42      0.00    133.12           RANKING
  23      1      1       -4.42      0.00    132.32           RANKING
  24      1     10       -4.39      0.00    133.64           RANKING
  24      2     44       -4.31      0.40    133.59           RANKING
  25      1     57       -4.38      0.00    133.42           RANKING
  25      2     48       -4.37      0.05    133.40           RANKING
  26      1     38       -4.36      0.00    132.77           RANKING
  27      1     56       -4.35      0.00    132.24           RANKING
  28      1     47       -4.32      0.00    132.80           RANKING
  29      1     79       -4.30      0.00    131.29           RANKING
  30      1     14       -4.27      0.00    132.53           RANKING
  30      2     93       -4.22      0.21    132.65           RANKING
  31      1     64       -4.27      0.00    133.37           RANKING
  31      2     45       -4.22      0.48    133.34           RANKING
  32      1     18       -4.23      0.00    137.02           RANKING
  33      1      8       -4.19      0.00    133.63           RANKING
  33      2     41       -4.10      0.44    133.79           RANKING
  34      1     61       -4.18      0.00    138.00           RANKING
  35      1      9       -4.16      0.00    133.01           RANKING
  36      1     58       -4.16      0.00    138.52           RANKING
  37      1     70       -4.15      0.00    132.55           RANKING
  37      2     49       -4.15      0.18    132.48           RANKING
  38      1     65       -4.14      0.00    133.38           RANKING
  39      1     19       -4.09      0.00    134.06           RANKING
  40      1     82       -3.96      0.00    130.54           RANKING
  41      1    100       -3.90      0.00    133.71           RANKING
  42      1     28       -3.85      0.00    133.29           RANKING
  43      1     63       -3.77      0.00    131.15           RANKING
  44      1      4       -3.72      0.00    131.54           RANKING
  45      1     87       -2.04      0.00    133.17           RANKING
_______________________________________________________________________