Whats the best way to measure / count number of
- SS bonds (Disulfide bond)
- hydrogen bonds
- Hydrophobic Bonds
- Ionic Bonds - Salt Bridges
from a pdb file. Is there any tools ?! I run DSSP on my pdb file, but there is always a warning regarding SSbonds, like the following, I played with the optimization parameter, but it didn't regulate the issue.
!!! Additional ssbond found between residues CYS 247 and CYS 253 !!!
Since, I am running DSSP on many pdf file, I need an accurate as well as safe method to count such bonds.