How can I compute energy from a protein PDB file?

  • Thread starter Thread starter user366312
  • Start date Start date
  • Tags 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.
user366312
Gold Member
Messages
88
Reaction score
3
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.

1696244256611.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)
 
Thread 'How to make Sodium Chlorate by Electrolysis of salt water?'

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 'Dissolving silver'

I'm making poor man's nitric acid to refine silver from scrap. I would like to waste as little as possible. I've noticed that about half the acid is destroyed oxidizing the metals, and I'd like to reduce that if possible. One reference mentioned that I lose only one in four in a "dilute solution" instead of half. How dilute must it be to allow the NO2 to disproportionate so that half of it will redissolve and become nitric acid again?
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 »

Similar threads

A Vacuum Energy from Correlation Functions
Replies
7
Views
2K
Python How can I retrieve integers from a file in Python?
Replies
8
Views
2K
How can I clone a USB drive to a VFD file for use in Windows?
Replies
14
Views
3K
Fortran How do I find an exact line from a large file in fortran90
Replies
16
Views
3K
How can I recover my .tex file after a computer crash?
Replies
9
Views
10K
I Is the Poynting Vector Field the Only Factor in Energy Flow in Circuits?
Replies
16
Views
3K
Admissions Statement of purpose critique request (high-energy theory PhD)
Replies
0
Views
2K
Fortran FORTRAN- How to read a non-uniformly formatted text file
Replies
3
Views
4K
I Will quantum computation lower energy requirements?
Replies
4
Views
7K
I Two-body correlation function computation
Replies
1
Views
3K

Hot Threads

Recent Insights

Back
Top