Body: <p>I have an sdf file of multiple ligands which is optimized previously with rdkit. Now I want to convert it to pdbqt format suitable for docking in one go - not manually and not with obabel. However the valencies should be satisfied correctly in the output when we add hydrogens.</p>
  <p>How can I do this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-13T13:10:56.230Z
Comments.Text: What about AutoDockTools? Also what languages are you familiar with? Python because I assume thats what is meant by RDKit? Are you looking for us to write the code for you (it's a fair amount of code) or just give advice? If you want us to write the code, generally we'd ask what code have your tried. Its not a hard task BTW, its just the way we answer things.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-14T13:37:44.123Z
Comments.Text: meaning you want us to suggest a library that does that ?? try this  https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#oddt.toolkits.extras.rdkit.MolToPDBQTBlock  from https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/tencent_8D4F6996C36D1BC76C22068BDE1C6664ED06%40qq.com/#msg36978353
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-14T14:28:28.697Z
Comments.Text: We wants advice...
Comments.UserDisplayName: Dikshit Rathva
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-26T15:57:50.777Z
Comments.Text: use one of various tools sdf->pdb, then pdb->pdbqt with autodock tools.
Comments.UserDisplayName: Maximilian Press
Tags: <docking><autodock>
Title: Conversion of multiple sdf files to pdbqt format
ThreadText: # Conversion of multiple sdf files to pdbqt format
  
  (Asked by: username_0 on 2024-12-13)
  
  I have an sdf file of multiple ligands which is optimized previously with rdkit. Now I want to convert it to pdbqt format suitable for docking in one go - not manually and not with obabel. However the valencies should be satisfied correctly in the output when we add hydrogens.
  
  How can I do this?
  
  **Tags:** docking, autodock
  
  > **Comments:**
  > **username_1**: What about AutoDockTools? Also what languages are you familiar with? Python because I assume thats what is meant by RDKit? Are you looking for us to write the code for you (it's a fair amount of code) or just give advice? If you want us to write the code, generally we'd ask what code have your tried. Its not a hard task BTW, its just the way we answer things.  
  > **username_2**: meaning you want us to suggest a library that does that ?? try this  https://oddt.readthedocs.io/en/latest/rst/oddt.toolkits.extras.rdkit.html#oddt.toolkits.extras.rdkit.MolToPDBQTBlock  from https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/tencent_8D4F6996C36D1BC76C22068BDE1C6664ED06%40qq.com/#msg36978353  
  > **username_0**: We wants advice...  
  > **username_3**: use one of various tools sdf->pdb, then pdb->pdbqt with autodock tools.  
  
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  ## 0 answers
  
  