Dear all,
I have a peptide with artificial amino acid (modified cysteine) and a linker. I attached the structure of unnatural amino acid and linker
May I know, is there a way to use Haddock for docking the system.
Thank you in advance!
The list of supported amino acids can be found at:
https://bianca.science.uu.nl/haddock2.4/library
Yours is not supported.
You could possibly define the addition to the cysteine as an HETATM residue, and define a distance restraint to keep the two sulphur atoms close to each other.
In that case you should change the residue name of the cysteine to CYC to allow a closer distance to the sulphur