How can I compute energy from a protein PDB file?

Thread starter user366312
Start date Oct 2, 2023
Tags

Energy Protein

AI Thread Summary

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.

Oct 2, 2023

user366312

Gold Member

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.

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)

Thread 'How to make Sodium Chlorate by Electrolysis of salt water?'

I have a power supply for electrolysis of salt water brine, variable 3v to 6v up to 30 amps. Cathode is stainless steel, anode is carbon rods. Carbon rod surface area 42" sq. the Stainless steel cathode should be 21" sq. Salt is pure 100% salt dissolved into distilled water. I have been making saturated salt wrong. Today I learn saturated salt is, dissolve pure salt into 150°f water cool to 100°f pour into the 2 gallon brine tank. I find conflicting information about brine tank...

View full post »

Thread 'Ruthenium-Iridium compound with catalytic effects'

Engineers slash iridium use in electrolyzer catalyst by 80%, boosting path to affordable green hydrogen https://news.rice.edu/news/2025/engineers-slash-iridium-use-electrolyzer-catalyst-80-boosting-path-affordable-green Ruthenium is also fairly expensive (a year ago it was about $490/ troy oz, but has nearly doubled in price over the past year, now about $910/ troy oz). I tracks prices of Pt, Pd, Ru, Ir and Ru. Of the 5 metals, rhodium (Rh) is the most expensive. A year ago, Rh and Ir...

View full post »