smina SDF files problems with ProLif and RdKit

Scoring and Minimization with AutoDock Vina

Status: Beta

Brought to you by: dkoes

smina SDF files problems with ProLif and RdKit

Forum: Help and Feedback

Creator: Syed Zayyan

Created: 2023-06-30

Updated: 2023-06-30

Syed Zayyan - 2023-06-30

hello!

I tried docking some compounds using SMINA. Scoring and SDF Files are generated however when reading them back into Python with RDkit I encounter this weird issue:

09:44:49] Explicit valence for atom # 9 N, 4, is greater than permitted
[09:44:49] ERROR: Could not sanitize molecule ending on line 55
[09:44:49] ERROR: Explicit valence for atom # 9 N, 4, is greater than permitted

However I can visualise the files using Chimera quite okay. which is utterly confusing!

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David Koes - 2023-06-30

Perhaps your molecule is charged with an extra hydrogen on the N but the charge set in the file? Without examples files and commondline, I can only speculate.

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- Syed Zayyan - 2023-06-30
  
  This is an example of the many. I am actually docking it to 6D9H, which is also attached.
  
  The SMILES: Cc1ccc(-c2nc(N)nc(N3CCN(C)CC3)n2)cc1
  
  Last edit: Syed Zayyan 2023-06-30
  
  6D9H_dockable.pdbqt
  
  CHEMBL3290580_docked_structure.sdf
  
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David Koes - 2023-06-30

You are probably using an older version of OpenBabel that doesn't Keukilize the molecules properly.

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- Syed Zayyan - 2023-06-30
  
  I don't think so............as in processing the .sdf files or initially when converting to PDBQT files
  
  Screenshot 2023-06-30 at 15.01.59.png
  
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David Koes - 2023-06-30

But what version is smina linked against?

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- Syed Zayyan - 2023-06-30
  
  I downloaded smina through conda and the only version of openbabel on conda list is :
  openbabel 3.1.1 py310h4b1c3e3_4 conda-forge
  
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- Syed Zayyan - 2023-06-30
  
  so only half of the molecules are acting this way and they do happen to come from another receptor but I don't see how that could have caused problems
  
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