Answers.Body: <p>You can do that with GROMACS. You probably need to check the manual for this, but roughly these are the steps:</p>
  <pre><code>gmx pdb2gmx -f input.pdb -o output.gro -water spc
  gmx solvate -cp output.gro -cs spc216.gro -o output_solv.gro -p output.top
  gmx pdb2gmx -f output_solv.gro -o output_processed.gro -p output.top -ignh
  gmx make_ndx -f output_processed.gro -o index.ndx
  gmx hbond -f output_processed.gro -n index.ndx -s output.tpr -num hbond.xvg -hbn hbond.ndx
  </code></pre>
  <p>First, you convert the PDB file into a GROMACS topology file using the pdb2gmx command. Then you can solvate the system with water molecules and add hydrogen atoms. Then you cCreate an index file containing the groups of atoms you want to analyze. Then you can use the hbond command to calculate the hydrogen bonds.</p>
  <p>I have not used GROMACS in a while. Hope that provides a starting point. With GROMACS you can even run a simulation and monitor the h-bonds over time.</p>
  <p>You actually might need to run an energy minimziation first, as the PDB might not in an optimal state for the h-bonds detection.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-08T08:27:16.037Z
Answers.Text: Great comment! I will keep this question open so that more possible answers can be added. Meanwhile, thank you for the suggestion! I will try and let you know!
Answers.UserDisplayName: Spartan 117
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-03T19:24:15.723Z
Answers.LastActivityDate: 2023-03-03T19:26:42.993Z
Answers.LastEditDate: 2023-03-03T19:26:42.993Z
Answers.UserDisplayName: Soerendip
Body: <p>I am analyzing the <a href="https://www.rcsb.org/3d-view/7VF2" rel="nofollow noreferrer">7VF2</a> structure, from the RCSB-database. I noticed that some residues belonging to one of its chains interact with the other chains that are present within the assembly. My question is if there is a method to extract a list of interacting residues that are present in a PDB.</p>
  <p>EDIT:
  <a href="https://i.sstatic.net/O39sF.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/O39sF.png" alt="enter image description here" /></a></p>
  <p>Just as an example, we have Lys 1616 belonging to ZC3H13 chain that interacts with Glu 621 of the protein virilizer homolog (the first chain)</p>
  <p>Mol* 3D visualizer can be used for major information in the 3D View in the link page I provided</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-02T14:14:31.177Z
Comments.Text: do you need alpha chain hydrogen interactions or side chains hydrogen interactions ? I believe most of the alpha helics and beta sheets emerge from apha carbon hydrogen bonds so thet'll be a huge number of interaction to be shown, but could be wrong
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-02T14:46:13.547Z
Comments.Text: https://files.rcsb.org/pub/pdb/validation_reports/vf/7vf2/7vf2_full_validation.pdf : Atom-1 Atom-2 Interatomic distance (Å) Clash overlap (Å) : 2:B:1616:LYS:HA 2:B:1616:LYS:HD2 1.71 0.42 there is something wrong with k1616 as per validation report states ... see atoms nomenclature in Lys http://ligand-expo.rcsb.org/reports/L/LYS/LYS_D3L3.gif
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-06T11:53:06.747Z
Comments.Text: DSSP gives you hydrogen bonds, not sure how it works for complexes though.
Comments.UserDisplayName: jgreener
Tags: <pdb><structural-biology>
Title: How to extract a list of hydrogen bonds from a PDB?
ThreadText: # How to extract a list of hydrogen bonds from a PDB?
  
  (Asked by: username_0 on 2023-03-01)
  
  I am analyzing the [7VF2](https://www.rcsb.org/3d-view/7VF2) structure, from the RCSB-database. I noticed that some residues belonging to one of its chains interact with the other chains that are present within the assembly. My question is if there is a method to extract a list of interacting residues that are present in a PDB.
  
  EDIT:
  [![enter image description here](https://i.sstatic.net/O39sF.png)](https://i.sstatic.net/O39sF.png)
  
  Just as an example, we have Lys 1616 belonging to ZC3H13 chain that interacts with Glu 621 of the protein virilizer homolog (the first chain)
  
  Mol\* 3D visualizer can be used for major information in the 3D View in the link page I provided
  
  **Tags:** pdb, structural-biology
  
  > **Comments:**
  > **username_1**: do you need alpha chain hydrogen interactions or side chains hydrogen interactions ? I believe most of the alpha helics and beta sheets emerge from apha carbon hydrogen bonds so thet'll be a huge number of interaction to be shown, but could be wrong  
  > **username_1**: https://files.rcsb.org/pub/pdb/validation_reports/vf/7vf2/7vf2_full_validation.pdf : Atom-1 Atom-2 Interatomic distance (Å) Clash overlap (Å) : 2:B:1616:LYS:HA 2:B:1616:LYS:HD2 1.71 0.42 there is something wrong with k1616 as per validation report states ... see atoms nomenclature in Lys http://ligand-expo.rcsb.org/reports/L/LYS/LYS_D3L3.gif  
  > **username_2**: DSSP gives you hydrogen bonds, not sure how it works for complexes though.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-03-03. Score: 1
  
  You can do that with GROMACS. You probably need to check the manual for this, but roughly these are the steps:
  
  ```
  gmx pdb2gmx -f input.pdb -o output.gro -water spc
  gmx solvate -cp output.gro -cs spc216.gro -o output_solv.gro -p output.top
  gmx pdb2gmx -f output_solv.gro -o output_processed.gro -p output.top -ignh
  gmx make_ndx -f output_processed.gro -o index.ndx
  gmx hbond -f output_processed.gro -n index.ndx -s output.tpr -num hbond.xvg -hbn hbond.ndx
  
  ```
  
  First, you convert the PDB file into a GROMACS topology file using the pdb2gmx command. Then you can solvate the system with water molecules and add hydrogen atoms. Then you cCreate an index file containing the groups of atoms you want to analyze. Then you can use the hbond command to calculate the hydrogen bonds.
  
  I have not used GROMACS in a while. Hope that provides a starting point. With GROMACS you can even run a simulation and monitor the h-bonds over time.
  
  You actually might need to run an energy minimziation first, as the PDB might not in an optimal state for the h-bonds detection.
  
  > **Comments:**
  > **username_0**: Great comment! I will keep this question open so that more possible answers can be added. Meanwhile, thank you for the suggestion! I will try and let you know!  
  
  ---
  
  