<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>

CC BY-SA 4.0
2023-09-29T15:24:48.183Z
https://mattermodeling.stackexchange.com/questions/11678/how-can-i-retrieve-bond-information-froma-protein-pdb-file
user366312
CC BY-SA 4.0
2023-09-29T17:11:59.310Z
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
pippo1980
CC BY-SA 4.0
2023-09-29T17:17:06.453Z
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
pippo1980
CC BY-SA 4.0
2023-09-29T17:18:16.783Z
think you'll need to create a dictionary for each residue
pippo1980
CC BY-SA 4.0
2023-09-29T19:03:29.607Z
see here for better explanation https://chemistry.stackexchange.com/a/162689/118509
pippo1980
<proteins><pdb>
How can I compute energy from a protein PDB file?
# 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

