Body: <p>Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file.</p>
  <p><a href="https://i.sstatic.net/qRIFG.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/qRIFG.png" alt="enter image description here" /></a></p>
  <p><strong>How can I do that?</strong></p>
  <p>Sometimes people suggest using the <code>CONECT</code> field for that purpose. However, some PDB files do not have this field.</p>
  <p>Example: <a href="https://www.rcsb.org/structure/4osk" rel="nofollow noreferrer">4OSK.pdb (Crystal structure of TAL effector reveals the recognition between asparagine and guanine)</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-29T15:24:48.183Z
Comments.Text: https://mattermodeling.stackexchange.com/questions/11678/how-can-i-retrieve-bond-information-froma-protein-pdb-file
Comments.UserDisplayName: user366312
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Comments.CreationDate: 2023-09-29T17:11:59.310Z
Comments.Text: https://www.ebi.ac.uk/pdbe-srv/pdbechem/bond/list/CYS Molecule : CYS    
  
  Bonds between two atoms of the molecule , then of course in each protein chain you'll have a Nterminal and Cterminal residues and all the ones in between having a peptide bond CO-N between Cter and Nter
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-29T17:17:06.453Z
Comments.Text: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=cys&operation=ccid here with pics http://ligand-expo.rcsb.org/reports/C/CYS/CYS_D3L1.gif
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-29T17:18:16.783Z
Comments.Text: think you'll need to create a dictionary for each residue
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-29T19:03:29.607Z
Comments.Text: see here for better explanation https://chemistry.stackexchange.com/a/162689/118509
Comments.UserDisplayName: pippo1980
Tags: <proteins><pdb>
Title: How can I compute energy from a protein PDB file?
ThreadText: # How can I compute energy from a protein PDB file?
  
  (Asked by: username_0 on 2023-09-29)
  
  Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file.
  
  [![enter image description here](https://i.sstatic.net/qRIFG.png)](https://i.sstatic.net/qRIFG.png)
  
  **How can I do that?**
  
  Sometimes people suggest using the `CONECT` field for that purpose. However, some PDB files do not have this field.
  
  Example: [4OSK.pdb (Crystal structure of TAL effector reveals the recognition between asparagine and guanine)](https://www.rcsb.org/structure/4osk)
  
  **Tags:** proteins, pdb
  
  > **Comments:**
  > **username_0**: https://mattermodeling.stackexchange.com/questions/11678/how-can-i-retrieve-bond-information-froma-protein-pdb-file  
  > **username_1**: https://www.ebi.ac.uk/pdbe-srv/pdbechem/bond/list/CYS Molecule : CYS      Bonds between two atoms of the molecule , then of course in each protein chain you'll have a Nterminal and Cterminal residues and all the ones in between having a peptide bond CO-N between Cter and Nter  
  > **username_1**: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=cys&operation=ccid here with pics http://ligand-expo.rcsb.org/reports/C/CYS/CYS_D3L1.gif  
  > **username_1**: think you'll need to create a dictionary for each residue  
  > **username_1**: see here for better explanation https://chemistry.stackexchange.com/a/162689/118509  
  
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  ## 0 answers
  
  