PLI error for pdb to pqr conversion

[zruan]

Hello developers,

I'm trying to use the ESP_DNN to calculate the ESP of a ligand molecule. The input pdb file looks like this:

HETATM    1  N   UNK C 601     122.444 122.637  75.742  0.00  0.00           N  
HETATM    2  N   UNK C 601     125.882 124.910  87.137  0.00  0.00           N  
HETATM    3  C   UNK C 601     123.711 123.036  79.714  0.00  0.00           C  
HETATM    4  C   UNK C 601     124.672 124.497  83.166  0.00  0.00           C  
HETATM    5  C   UNK C 601     124.651 122.923  78.689  0.00  0.00           C  
HETATM    6  C   UNK C 601     123.715 124.539  84.168  0.00  0.00           C  
HETATM    7  C   UNK C 601     124.107 123.177  81.109  0.00  0.00           C  
HETATM    8  C   UNK C 601     124.290 124.354  81.750  0.00  0.00           C  
HETATM    9  C   UNK C 601     122.349 123.013  79.415  0.00  0.00           C  
HETATM   10  C   UNK C 601     126.024 124.589  83.460  0.00  0.00           C  
HETATM   11  C   UNK C 601     124.229 122.790  77.367  0.00  0.00           C  
HETATM   12  C   UNK C 601     124.119 124.677  85.496  0.00  0.00           C  
HETATM   13  C   UNK C 601     122.867 122.769  77.069  0.00  0.00           C  
HETATM   14  C   UNK C 601     125.476 124.770  85.806  0.00  0.00           C  
HETATM   15  C   UNK C 601     121.926 122.880  78.093  0.00  0.00           C  
HETATM   16  C   UNK C 601     126.428 124.727  84.788  0.00  0.00           C  
HETATM   17  C   UNK C 601     122.310 123.672  75.190  0.00  0.00           C  
HETATM   18  C   UNK C 601     126.070 123.878  87.678  0.00  0.00           C  
HETATM   19  O   UNK C 601     126.700 124.480  79.466  0.00  0.00           O  
HETATM   20  O   UNK C 601     121.762 122.882  83.355  0.00  0.00           O  
HETATM   21  O   UNK C 601     126.620 122.096  80.166  0.00  0.00           O  
HETATM   22  O   UNK C 601     127.039 122.694  77.744  0.00  0.00           O  
HETATM   23  O   UNK C 601     121.289 124.599  85.089  0.00  0.00           O  
HETATM   24  O   UNK C 601     121.737 125.298  82.700  0.00  0.00           O  
HETATM   25  S   UNK C 601     126.374 122.945  79.011  0.00  0.00           S  
HETATM   26  S   UNK C 601     121.999 124.426  83.833  0.00  0.00           S  
HETATM   27  S   UNK C 601     122.122 125.054  74.420  0.00  0.00           S  
HETATM   28  S   UNK C 601     126.332 122.498  88.432  0.00  0.00           S  
HETATM   29  H   UNK C 601     124.233 122.243  81.651  0.00  0.00           H  
HETATM   30  H   UNK C 601     124.163 125.291  81.212  0.00  0.00           H  
HETATM   31  H   UNK C 601     121.601 123.098  80.201  0.00  0.00           H  
HETATM   32  H   UNK C 601     126.780 124.556  82.680  0.00  0.00           H  
HETATM   33  H   UNK C 601     124.941 122.702  76.550  0.00  0.00           H  
HETATM   34  H   UNK C 601     123.396 124.714  86.307  0.00  0.00           H  
HETATM   35  H   UNK C 601     120.863 122.862  77.872  0.00  0.00           H  
HETATM   36  H   UNK C 601     127.489 124.800  85.017  0.00  0.00           H  
HETATM   37  H   UNK C 601     126.522 124.698  80.408  0.00  0.00           H  
HETATM   38  H   UNK C 601     121.993 122.193  84.021  0.00  0.00           H  
CONECT    1   13   17
CONECT    2   14   18
CONECT    3    5    7    9
CONECT    4    6    8   10
CONECT    5    3   11   25
CONECT    6    4   12   26
CONECT    7    3    8   29
CONECT    8    4    7   30
CONECT    9    3   15   31
CONECT   10    4   16   32
CONECT   11    5   13   33
CONECT   12    6   14   34
CONECT   13    1   11   15
CONECT   14    2   12   16
CONECT   15    9   13   35
CONECT   16   10   14   36
CONECT   17    1   27
CONECT   18    2   28
CONECT   19   37   25
CONECT   20   38   26
CONECT   21   25
CONECT   22   25
CONECT   23   26
CONECT   24   26
CONECT   25    5   19   21   22
CONECT   26    6   20   23   24
CONECT   27   17
CONECT   28   18
CONECT   29    7
CONECT   30    8
CONECT   31    9
CONECT   32   10
CONECT   33   11
CONECT   34   12
CONECT   35   15
CONECT   36   16
CONECT   37   19
CONECT   38   20
END

After running python -m esp_dnn.predict -m ligand -i examples/px1_drugs/, I got the following error:

[predict:INFO] Ruuning in ligand mode
[predict:INFO] Input dir is /legacy/storage/projects/lu/Zheng/software/ESP_DNN/examples/px1_drugs
[predict:INFO] Output dir is /legacy/storage/projects/lu/Zheng/software/ESP_DNN/examples/px1_drugs
[predict:INFO] Loading the trained model from /legacy/storage/projects/lu/Zheng/software/ESP_DNN/esp_dnn/model directory
Using TensorFlow backend.
2023-04-09 17:47:31.377224: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 AVX512F FMA
[predict:INFO] /legacy/storage/projects/lu/Zheng/software/ESP_DNN/examples/px1_drugs/dids.pdb -> /legacy/storage/projects/lu/Zheng/software/ESP_DNN/examples/px1_drugs/dids.pdb.pqr
[predict:ERROR] Error converting /legacy/storage/projects/lu/Zheng/software/ESP_DNN/examples/px1_drugs/dids.pdb file
[predict:ERROR] PLI failed to create pqr file
PLI Error:
Fatal error:
set_fgroup_type: matched fgroup type does not match hydrogens for atom ligand:7

The error message is not very informative to me. Do you know what might be wrong in this case?

Thank you so much!

[fredludlow]

I suspect it's the odd geometry around that central double bond? (atoms 7 and 8). It might help to have an input file with double bonds specified using the (unofficial) multiple CONECT record format, e.g. there's a double bond between 7 and 8 so it would look like:

CONECT    7    3    8    8   29
CONECT    8    4    7    7   30