CHARMM Development Project Forums User Discussion & Questions General Chemistry Discussions Sulphur

Is there significant difference between Sulphur-sulphur bond in the element vs disulphide bond length in protein?

So if inter sulphur distance is less than than a threshold, do we take it to exist?

In Pdb files, bonds are described. Why are suphide patches done in CHARMM then? Because some sulphur atoms are missing?

In an empirical force field it is necessary to explicity define all bonds. in CHARMM, this information is NOT obtained from a PDB file, bur rather from the RTF file and subsequent GENERATE and PATCH statements. in the case of disulfides, the initial GENERATE statement will create the standard amino acids, including CYS, in a polypeptide chain. the subsequent PATCH statement to create the disulfide is necessary to remove the HG atoms on CYS and create the actual disulfide bond.

alex

Does that mean the norm is to check whether disulphide bond is present in the pdb, then explicitly patch the bond in CHARMM?

yes