How can I compute energy from a protein PDB file?

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To compute energy from a protein PDB file using coordinates, it's essential to understand the role of the `CONECT` field, which specifies connectivity between atoms. However, not all PDB files include this field, which can complicate energy calculations. For example, the PDB file 4OSK, detailing the crystal structure of a TAL effector, may lack the necessary connectivity information. In such cases, alternative methods for determining atom connections must be employed, such as using predefined bonding rules based on atom types or utilizing software tools that can infer connectivity from the atomic coordinates provided in the PDB file. This approach ensures accurate energy computation even in the absence of the `CONECT` field.
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TL;DR Summary
Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file.

**How can I do that?**
Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in that file.

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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)
 

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