<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>

CC BY-SA 4.0
2024-11-20T14:34:03.050Z
2024-11-20T14:34:03.050Z
Muhammad Radifar
<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>

CC BY-SA 4.0
2024-11-20T20:23:37.427Z
2024-11-20T20:23:37.427Z
Maximilian Press
<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>

CC BY-SA 4.0
2023-10-19T09:16:26.157Z
Try reopen in biopythown and save pdb  with preserve_atom_numbering = False
pippo1980
CC BY-SA 4.0
2023-10-19T09:17:22.263Z
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
pippo1980
CC BY-SA 4.0
2023-10-19T09:22:31.903Z
See https://www.mail-archive.com/openbabel-discuss@lists.sourceforge.net/msg05790.html
pippo1980
CC BY-SA 4.0
2023-10-19T10:36:50.980Z
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
pippo1980
CC BY-SA 4.0
2023-10-19T12:16:19.123Z
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
pippo1980
CC BY-SA 4.0
2023-10-19T12:26:10.777Z
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.
pippo1980
CC BY-SA 4.0
2023-10-19T12:43:38.440Z
https://kpwulab.com/2021/02/19/pymolchimeraadd-hydrogens-to-your-structure/ chimera should work fine
pippo1980
<proteins><docking><format-conversion>
Renumbering atoms in PDB using OpenBabel
# 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  

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## 2 answers

### Answer by username_2 on 2024-11-20. Score: 1

I wrote [PiLAH](https://github.com/radifar/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.


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### 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.


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