Answers.Body: <p>I wrote <a href="https://github.com/radifar/pilah" rel="nofollow noreferrer">PiLAH</a>, which can generate PDBQT file from PDB with the renumbered hydrogen atom index so that the hydrogen appear right below the heavy atoms. It is not right below its corresponding heavy atom though.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-20T14:34:03.050Z
Answers.LastActivityDate: 2024-11-20T14:34:03.050Z
Answers.UserDisplayName: Muhammad Radifar
Answers.Body: <p>ADFRSuite has a command/script <code>prepare_receptor</code> as documented <a href="https://autodock-vina.readthedocs.io/en/latest/docking_basic.html#preparing-the-receptor" rel="nofollow noreferrer">here</a> that performs a lot of these steps including pdbqt conversion in preparation for docking. Note that this is intended for Autodock / Vina and other tools may have different format needs.</p>
  <p>I would recommend using this workflow if you are using AutoDock.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-20T20:23:37.427Z
Answers.LastActivityDate: 2024-11-20T20:23:37.427Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I'm trying to add polar hydrogens to protein (PDB ID 3l3l cleaned from water and ligands) and convert it to PDBQT using OpenBabel by:
  <code>obabel -ipdb target.pdb -opdbqt -O target.pdbqt -xr --partialcharge gasteiger --addpolarh</code>
  It's working well, but all hydrogens are appending to the end of file. I want to renumber atoms so that residues in PDB would go in increasing order and hydrogens were located &quot;between&quot; corresponding heavy atoms, like AutoDock Tools do this.</p>
  <p>Is there a way to renumber them using OpenBabel? Or any other command-line utilities?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T09:16:26.157Z
Comments.Text: Try reopen in biopythown and save pdb  with preserve_atom_numbering = False
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T09:17:22.263Z
Comments.Text: Please add a small bit of the pdb with non ordered H so that people can try to help you without having to spend too much time
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T09:22:31.903Z
Comments.Text: See https://www.mail-archive.com/openbabel-discuss@lists.sourceforge.net/msg05790.html
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T10:36:50.980Z
Comments.Text: I see the prob openbabel ( at least this one https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html  OPEN BABEL 3.1.1) doesnt name the Hs correctly (their are all just H) so that biopython parser drops them as duplicates. Use pymol h_add to a pdb then save directly from pymol or run conversion in openbabel
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T12:16:19.123Z
Comments.Text: mmmmh even my pymol assigns wrong names to H atoms compared to the ones in the https://www.ebi.ac.uk/pdbe-srv/pdbechem/ or http://ligand-expo.rcsb.org/ld-search.html
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T12:26:10.777Z
Comments.Text: https://phenix-online.org/documentation/reference/ready_set.html ReadySet! is a program designed to prepare a PDB file for refinement as in ReadySet! Refine!!!. It will add hydrogens to the protein model using phenix.reduce and to the ligands using eLBOW. The appropriate restraints are also written to disk. Hydrogens can also be added to water molecules. Deuterium atoms can be added to facilitate dual xray-neutron refinement. Metal coordination files are also generated.
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-19T12:43:38.440Z
Comments.Text: https://kpwulab.com/2021/02/19/pymolchimeraadd-hydrogens-to-your-structure/ chimera should work fine
Comments.UserDisplayName: pippo1980
Tags: <proteins><docking><format-conversion>
Title: Renumbering atoms in PDB using OpenBabel
ThreadText: # Renumbering atoms in PDB using OpenBabel
  
  (Asked by: username_0 on 2023-10-19)
  
  I'm trying to add polar hydrogens to protein (PDB ID 3l3l cleaned from water and ligands) and convert it to PDBQT using OpenBabel by:
  `obabel -ipdb target.pdb -opdbqt -O target.pdbqt -xr --partialcharge gasteiger --addpolarh`
  It's working well, but all hydrogens are appending to the end of file. I want to renumber atoms so that residues in PDB would go in increasing order and hydrogens were located "between" corresponding heavy atoms, like AutoDock Tools do this.
  
  Is there a way to renumber them using OpenBabel? Or any other command-line utilities?
  
  **Tags:** proteins, docking, format-conversion
  
  > **Comments:**
  > **username_1**: Try reopen in biopythown and save pdb  with preserve_atom_numbering = False  
  > **username_1**: Please add a small bit of the pdb with non ordered H so that people can try to help you without having to spend too much time  
  > **username_1**: See https://www.mail-archive.com/openbabel-discuss@lists.sourceforge.net/msg05790.html  
  > **username_1**: I see the prob openbabel ( at least this one https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html  OPEN BABEL 3.1.1) doesnt name the Hs correctly (their are all just H) so that biopython parser drops them as duplicates. Use pymol h_add to a pdb then save directly from pymol or run conversion in openbabel  
  > **username_1**: mmmmh even my pymol assigns wrong names to H atoms compared to the ones in the https://www.ebi.ac.uk/pdbe-srv/pdbechem/ or http://ligand-expo.rcsb.org/ld-search.html  
  > **username_1**: https://phenix-online.org/documentation/reference/ready_set.html ReadySet! is a program designed to prepare a PDB file for refinement as in ReadySet! Refine!!!. It will add hydrogens to the protein model using phenix.reduce and to the ligands using eLBOW. The appropriate restraints are also written to disk. Hydrogens can also be added to water molecules. Deuterium atoms can be added to facilitate dual xray-neutron refinement. Metal coordination files are also generated.  
  > **username_1**: https://kpwulab.com/2021/02/19/pymolchimeraadd-hydrogens-to-your-structure/ chimera should work fine  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2024-11-20. Score: 1
  
  I wrote [PiLAH](https://github.com/username_2/pilah), which can generate PDBQT file from PDB with the renumbered hydrogen atom index so that the hydrogen appear right below the heavy atoms. It is not right below its corresponding heavy atom though.
  
  
  ---
  
  ### Answer by username_3 on 2024-11-20. Score: 0
  
  ADFRSuite has a command/script `prepare_receptor` as documented [here](https://autodock-vina.readthedocs.io/en/latest/docking_basic.html#preparing-the-receptor) that performs a lot of these steps including pdbqt conversion in preparation for docking. Note that this is intended for Autodock / Vina and other tools may have different format needs.
  
  I would recommend using this workflow if you are using AutoDock.
  
  
  ---
  
  