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Unable to output file #669

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fishbig2017 opened this issue Feb 28, 2025 · 3 comments
Open

Unable to output file #669

fishbig2017 opened this issue Feb 28, 2025 · 3 comments

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@fishbig2017
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fishbig2017 commented Feb 28, 2025 •
edited by pckroon
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hello there vermouth-martinize people!

When I was using the command：
Martinize2-f protein-pdb - o topol. top - x cgsprotein. pdb - ff Martini3001

encountered the problem:

    INFO - general - Read 1 molecules from PDB file protein.pdb
    INFO - step - Guessing the bonds.
 WARNING - unknown-residue - Can't add bonds based on atom names for residue -1 because 'Residue  is not known to force field charmm'. Falling back to distance criteria.
    INFO - general - 1 molecules after guessing bonds
 WARNING - general - Residue specified by "cter" for mutation "C-ter" not found
    INFO - step - Repairing the graph.
 WARNING - unknown-residue - Cannot recognize residue '' in  molecule 0. Deleting the molecule.
    INFO - step - Dealing with modifications.
    INFO - step - Read input.
    INFO - step - Creating the graph at the target resolution.
    INFO - step - Averaging the coordinates.
    INFO - step - Applying the links.
    INFO - step - Placing the charge dummies.
    INFO - step - Sorting atomids
    INFO - step - Writing output.
Traceback (most recent call last):
  File "D:\conda\Scripts\martinize2-script.py", line 1199, in <module>
    entry()
  File "D:\conda\Scripts\martinize2-script.py", line 1170, in entry
    write_gmx_topology(system,
  File "D:\conda\Lib\site-packages\vermouth\gmx\topology.py", line 148, in write_gmx_topology
    raise ValueError("No molecule in the system. Nothing to write.")
ValueError: No molecule in the system. Nothing to write.

The workstation with python3.12.3
The vermouth version is: vermouth-0.13.1.dev40
@pckroon
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pckroon commented Feb 28, 2025

Hi,
your command line doens't make much sense, there's spaces all over. Could you exactly copy-paste your command line next time, instead of typing what you think your command was?
In addition, I think there's something wrong with your input protein.pdb. Could you share a few lines of that?

@fishbig2017
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fishbig2017 commented Feb 28, 2025 •
edited by pckroon
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The input command is this:
martinize2 -f protein.pdb -o topol.top -x cg_protein.pdb-ff martini3001

I don't know why the copy to github above the appearance of these extra Spaces.The protein.pdb information is as follows:

ATOM      1  P1  MOL     1       6.084  -7.058  -0.329  1.00  0.00           P    
ATOM      2  O2  MOL     1       4.600  -8.074  -0.105  1.00  0.00           O    
ATOM      3  O3  MOL     1       8.984  -7.510  -0.883  1.00  0.00           O    
ATOM      4  O4  MOL     1       8.835  -4.499   1.332  1.00  0.00           O    
ATOM      5  O5  MOL     1       6.780  -6.884   1.360  1.00  0.00           O    
ATOM      6  O6  MOL     1      10.901  -5.980  -1.753  1.00  0.00           O    
ATOM      7  O7  MOL     1       7.521  -2.531   0.201  1.00  0.00           O    
ATOM      8  O8  MOL     1       5.602  -5.376  -0.900  1.00  0.00           O1-  
ATOM      9  O9  MOL     1       6.906  -7.995  -1.679  1.00  0.00           O    
ATOM     10  N10 MOL     1       1.385  -6.537   0.172  1.00  0.00           N1+  
ATOM     11  C11 MOL     1      16.718  -6.404  -0.399  1.00  0.00           C    
ATOM     12  C12 MOL     1      18.032  -5.674  -0.303  1.00  0.00           C    
ATOM     13  C13 MOL     1      13.804   1.485  -0.008  1.00  0.00           C    
ATOM     14  C14 MOL     1      13.305   2.890  -0.198  1.00  0.00           C    
ATOM     15  C15 MOL     1      15.691  -5.294  -0.291  1.00  0.00           C    
ATOM     16  C16 MOL     1      18.993  -6.833  -0.135  1.00  0.00           C    
ATOM     17  C17 MOL     1      12.463   0.939   0.372  1.00  0.00           C    
ATOM     18  C18 MOL     1      14.689   3.468  -0.235  1.00  0.00           C    
ATOM     19  C19 MOL     1      14.626  -6.296   0.090  1.00  0.00           C    
ATOM     20  C20 MOL     1      20.213  -5.952  -0.011  1.00  0.00           C    
ATOM     21  C21 MOL     1      12.849  -0.489   0.649  1.00  0.00           C    
ATOM     22  C22 MOL     1      14.322   4.923  -0.125  1.00  0.00           C    
ATOM     23  C23 MOL     1      13.698  -5.723   1.154  1.00  0.00           C    
ATOM     24  C24 MOL     1      11.390  -0.816   0.522  1.00  0.00           C    
ATOM     25  C25 MOL     1      21.387  -6.903   0.009  1.00  0.00           C    
ATOM     26  C26 MOL     1      15.736   5.449  -0.084  1.00  0.00           C    
ATOM     27  C27 MOL     1      12.990  -7.054   1.363  1.00  0.00           C    
ATOM     28  C28 MOL     1      11.405  -2.236   0.028  1.00  0.00           C    
ATOM     29  C29 MOL     1      22.507  -5.877   0.023  1.00  0.00           C    
ATOM     30  C30 MOL     1      15.477   6.937  -0.002  1.00  0.00           C    
ATOM     31  C31 MOL     1       2.335  -7.655  -0.107  1.00  0.00           C    
ATOM     32  C32 MOL     1      12.184  -6.922   0.077  1.00  0.00           C    
ATOM     33  C33 MOL     1      10.088  -2.055  -0.705  1.00  0.00           C    
ATOM     34  C34 MOL     1      23.748  -6.753   0.002  1.00  0.00           C    
ATOM     35  C35 MOL     1      16.900   7.467  -0.009  1.00  0.00           C    
ATOM     36  C36 MOL     1       0.762  -5.943  -1.067  1.00  0.00           C    
ATOM     37  C37 MOL     1       0.385  -7.191   1.086  1.00  0.00           C    
ATOM     38  C38 MOL     1       2.155  -5.464   0.907  1.00  0.00           C    
ATOM     39  C39 MOL     1       3.639  -7.035  -0.576  1.00  0.00           C    
ATOM     40  C40 MOL     1      11.392  -8.141  -0.360  1.00  0.00           C    
ATOM     41  C41 MOL     1       9.670  -3.484  -0.936  1.00  0.00           C    
ATOM     42  C42 MOL     1      24.947  -5.808   0.044  1.00  0.00           C    
ATOM     43  C43 MOL     1      16.750   8.983   0.061  1.00  0.00           C    
ATOM     44  C44 MOL     1       9.066  -7.028   0.540  1.00  0.00           C    
ATOM     45  C45 MOL     1      10.426  -7.300  -1.183  1.00  0.00           C    
ATOM     46  C46 MOL     1      26.157  -6.749   0.054  1.00  0.00           C    
ATOM     47  C47 MOL     1       8.691  -3.479   0.241  1.00  0.00           C    
ATOM     48  C48 MOL     1      18.189   9.509   0.063  1.00  0.00           C    
ATOM     49  C49 MOL     1       8.831  -5.546   0.266  1.00  0.00           C    
ATOM     50  C50 MOL     1       8.077  -7.609   1.553  1.00  0.00           C    
ATOM     51  H51 MOL     1      16.631  -7.054   0.538  1.00  0.00           H    
ATOM     52  H52 MOL     1      16.608  -7.049  -1.328  1.00  0.00           H    
ATOM     53  H53 MOL     1      18.059  -5.017   0.624  1.00  0.00           H    
ATOM     54  H54 MOL     1      18.250  -5.059  -1.241  1.00  0.00           H    
ATOM     55  H55 MOL     1      14.523   1.409   0.869  1.00  0.00           H    
ATOM     56  H56 MOL     1      14.247   1.031  -0.959  1.00  0.00           H    
ATOM     57  H57 MOL     1      12.756   3.241   0.744  1.00  0.00           H    
ATOM     58  H58 MOL     1      12.684   3.059  -1.132  1.00  0.00           H    
ATOM     59  H59 MOL     1      15.499  -4.669  -1.232  1.00  0.00           H    
ATOM     60  H60 MOL     1      15.964  -4.653   0.604  1.00  0.00           H    
ATOM     61  H61 MOL     1      19.019  -7.492  -1.060  1.00  0.00           H    
ATOM     62  H62 MOL     1      18.801  -7.446   0.812  1.00  0.00           H    
ATOM     63  H63 MOL     1      11.771   1.013  -0.533  1.00  0.00           H    
ATOM     64  H64 MOL     1      11.994   1.445   1.279  1.00  0.00           H    
ATOM     65  H65 MOL     1      15.248   3.203  -1.200  1.00  0.00           H    
ATOM     66  H66 MOL     1      15.278   3.143   0.678  1.00  0.00           H    
ATOM     67  H67 MOL     1      15.175  -7.128   0.649  1.00  0.00           H    
ATOM     68  H68 MOL     1      14.134  -6.755  -0.826  1.00  0.00           H    
ATOM     69  H69 MOL     1      20.168  -5.318   0.932  1.00  0.00           H    
ATOM     70  H70 MOL     1      20.285  -5.279  -0.932  1.00  0.00           H    
ATOM     71  H71 MOL     1      13.359  -0.716   1.648  1.00  0.00           H    
ATOM     72  H72 MOL     1      13.424  -0.892  -0.243  1.00  0.00           H    
ATOM     73  H73 MOL     1      13.758   5.145   0.848  1.00  0.00           H    
ATOM     74  H74 MOL     1      13.743   5.284  -1.030  1.00  0.00           H    
ATOM     75  H75 MOL     1      13.000  -4.899   0.777  1.00  0.00           H    
ATOM     76  H76 MOL     1      14.300  -5.395   2.060  1.00  0.00           H    
ATOM     77  H77 MOL     1      11.012  -0.191  -0.357  1.00  0.00           H    
ATOM     78  H78 MOL     1      10.747  -0.610   1.436  1.00  0.00           H    
ATOM     79  H79 MOL     1      21.418  -7.534  -0.937  1.00  0.00           H    
ATOM     80  H80 MOL     1      21.387  -7.564   0.942  1.00  0.00           H    
ATOM     81  H81 MOL     1      16.293   5.175  -1.046  1.00  0.00           H    
ATOM     82  H82 MOL     1      16.296   5.063   0.826  1.00  0.00           H    
ATOM     83  H83 MOL     1      12.302  -7.092   2.271  1.00  0.00           H    
ATOM     84  H84 MOL     1      13.746  -7.907   1.358  1.00  0.00           H    
ATOM     85  H85 MOL     1      11.435  -2.975   0.900  1.00  0.00           H    
ATOM     86  H86 MOL     1      12.217  -2.440  -0.740  1.00  0.00           H    
ATOM     87  H87 MOL     1      22.458  -5.244   0.967  1.00  0.00           H    
ATOM     88  H88 MOL     1      22.457  -5.211  -0.905  1.00  0.00           H    
ATOM     89  H89 MOL     1      14.927   7.203   0.965  1.00  0.00           H    
ATOM     90  H90 MOL     1      14.894   7.294  -0.909  1.00  0.00           H    
ATOM     91  H91 MOL     1       1.937  -8.468  -0.801  1.00  0.00           H    
ATOM     92  H92 MOL     1       2.568  -8.111   0.911  1.00  0.00           H    
ATOM     93  H93 MOL     1      12.826  -6.602  -0.809  1.00  0.00           H    
ATOM     94  H94 MOL     1      11.439  -6.087   0.292  1.00  0.00           H    
ATOM     95  H95 MOL     1      10.263  -1.449  -1.657  1.00  0.00           H    
ATOM     96  H96 MOL     1       9.314  -1.555  -0.039  1.00  0.00           H    
ATOM     97  H97 MOL     1      23.764  -7.382  -0.946  1.00  0.00           H    
ATOM     98  H98 MOL     1      23.749  -7.433   0.920  1.00  0.00           H    
ATOM     99  H99 MOL     1      17.429   7.155  -0.972  1.00  0.00           H    
ATOM    100 0H10 MOL     1      17.469   7.072   0.894  1.00  0.00           H    
ATOM    101 1H10 MOL     1       0.204  -6.755  -1.639  1.00  0.00           H    
ATOM    102 2H10 MOL     1       1.576  -5.499  -1.731  1.00  0.00           H    
ATOM    103 3H10 MOL     1       0.032  -5.123  -0.761  1.00  0.00           H    
ATOM    104 4H10 MOL     1       0.946  -7.626   1.979  1.00  0.00           H    
ATOM    105 5H10 MOL     1      -0.140  -8.035   0.526  1.00  0.00           H    
ATOM    106 6H10 MOL     1      -0.377  -6.426   1.447  1.00  0.00           H    
ATOM    107 7H10 MOL     1       2.942  -5.021   0.210  1.00  0.00           H    
ATOM    108 8H10 MOL     1       2.673  -5.920   1.814  1.00  0.00           H    
ATOM    109 9H10 MOL     1       1.443  -4.640   1.244  1.00  0.00           H    
ATOM    110 0H11 MOL     1       3.677  -6.810  -1.693  1.00  0.00           H    
ATOM    111 1H11 MOL     1       3.861  -6.096   0.029  1.00  0.00           H    
ATOM    112 2H11 MOL     1      10.823  -8.593   0.522  1.00  0.00           H    
ATOM    113 3H11 MOL     1      12.001  -8.916  -0.928  1.00  0.00           H    
ATOM    114 4H11 MOL     1      10.557  -4.199  -0.814  1.00  0.00           H    
ATOM    115 5H11 MOL     1       9.109  -3.622  -1.911  1.00  0.00           H    
ATOM    116 6H11 MOL     1      24.915  -5.178   0.992  1.00  0.00           H    
ATOM    117 7H11 MOL     1      24.954  -5.135  -0.877  1.00  0.00           H    
ATOM    118 8H11 MOL     1      16.207   9.277   1.020  1.00  0.00           H    
ATOM    119 9H11 MOL     1      16.176   9.361  -0.848  1.00  0.00           H    
ATOM    120 0H12 MOL     1      10.120  -7.227   0.926  1.00  0.00           H    
ATOM    121 1H12 MOL     1      26.139  -7.385  -0.891  1.00  0.00           H    
ATOM    122 2H12 MOL     1      26.090  -7.426   0.969  1.00  0.00           H    
ATOM    123 3H12 MOL     1      27.117  -6.137   0.093  1.00  0.00           H    
ATOM    124 4H12 MOL     1      18.709   9.170  -0.893  1.00  0.00           H    
ATOM    125 5H12 MOL     1      18.737   9.082   0.966  1.00  0.00           H    
ATOM    126 6H12 MOL     1      18.177  10.647   0.117  1.00  0.00           H    
ATOM    127 7H12 MOL     1       9.647  -5.282  -0.473  1.00  0.00           H    
ATOM    128 8H12 MOL     1       7.834  -5.419  -0.270  1.00  0.00           H    
ATOM    129 9H12 MOL     1       7.993  -8.741   1.439  1.00  0.00           H    
ATOM    130 0H13 MOL     1       8.440  -7.353   2.602  1.00  0.00           H    
TER     131 
CONECT    1    2    5    8    9
CONECT    2    1   39
CONECT    3   44   45
CONECT    4   47   49
CONECT    5    1   50
CONECT    6   45
CONECT    7   47
CONECT    8    1
CONECT    9    1
CONECT   10   31   36   37   38
CONECT   11   12   15   51   52
CONECT   12   11   16   53   54
CONECT   13   14   17   55   56
CONECT   14   13   18   57   58
CONECT   15   11   19   59   60
CONECT   16   12   20   61   62
CONECT   17   13   21   63   64
CONECT   18   14   22   65   66
CONECT   19   15   23   67   68
CONECT   20   16   25   69   70
CONECT   21   17   24   71   72
CONECT   22   18   26   73   74
CONECT   23   19   27   75   76
CONECT   24   21   28   77   78
CONECT   25   20   29   79   80
CONECT   26   22   30   81   82
CONECT   27   23   32   83   84
CONECT   28   24   33   85   86
CONECT   29   25   34   87   88
CONECT   30   26   35   89   90
CONECT   31   10   39   91   92
CONECT   32   27   40   93   94
CONECT   33   28   41   95   96
CONECT   34   29   42   97   98
CONECT   35   30   43   99  100
CONECT   36   10  101  102  103
CONECT   37   10  104  105  106
CONECT   38   10  107  108  109
CONECT   39    2   31  110  111
CONECT   40   32   45  112  113
CONECT   41   33   47  114  115
CONECT   42   34   46  116  117
CONECT   43   35   48  118  119
CONECT   44    3   49   50  120
CONECT   45    3    6   40
CONECT   46   42  121  122  123
CONECT   47    4    7   41
CONECT   48   43  124  125  126
CONECT   49    4   44  127  128
CONECT   50    5   44  129  130
CONECT   51   11
CONECT   52   11
CONECT   53   12
CONECT   54   12
CONECT   55   13
CONECT   56   13
CONECT   57   14
CONECT   58   14
CONECT   59   15
CONECT   60   15
CONECT   61   16
CONECT   62   16
CONECT   63   17
CONECT   64   17
CONECT   65   18
CONECT   66   18
CONECT   67   19
CONECT   68   19
CONECT   69   20
CONECT   70   20
CONECT   71   21
CONECT   72   21
CONECT   73   22
CONECT   74   22
CONECT   75   23
CONECT   76   23
CONECT   77   24
CONECT   78   24
CONECT   79   25
CONECT   80   25
CONECT   81   26
CONECT   82   26
CONECT   83   27
CONECT   84   27
CONECT   85   28
CONECT   86   28
CONECT   87   29
CONECT   88   29
CONECT   89   30
CONECT   90   30
CONECT   91   31
CONECT   92   31
CONECT   93   32
CONECT   94   32
CONECT   95   33
CONECT   96   33
CONECT   97   34
CONECT   98   34
CONECT   99   35
CONECT  100   35
CONECT  101   36
CONECT  102   36
CONECT  103   36
CONECT  104   37
CONECT  105   37
CONECT  106   37
CONECT  107   38
CONECT  108   38
CONECT  109   38
CONECT  110   39
CONECT  111   39
CONECT  112   40
CONECT  113   40
CONECT  114   41
CONECT  115   41
CONECT  116   42
CONECT  117   42
CONECT  118   43
CONECT  119   43
CONECT  120   44
CONECT  121   46
CONECT  122   46
CONECT  123   46
CONECT  124   48
CONECT  125   48
CONECT  126   48
CONECT  127   49
CONECT  128   49
CONECT  129   50
CONECT  130   50
END

@pckroon
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pckroon commented Feb 28, 2025

Thanks.

So, your residue is called MOL, and as the warning said, martinize2 doesn't know a residue called MOL. Please have a look at the documentation, for example at https://vermouth-martinize.readthedocs.io/en/latest/tutorials/6_adding_residues_links/index.html

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