Molecular Dynamics

DISULFIDE BONDS GROMACS

1. Disulfide bonds. Disulfide bonds are usually important for protein structural stability or function. It would be good to have a look at this particular information in the literature before setting up an MD.  PDB file also provides information on SSBOND section.

• Scenario 1: You know a disulfide bond should be present in your protein. There is specbond.dat file in the forcefield that contains the information of how a bond is defined. A disulfide bond is defined between 2 sulfur atoms that are between 1.8 and 2.2 angstroms apart. So the algorithm will automatically detect these cases in your coordinate file. You can utilize the -ss flag with pdb2gmx to interactively ensure a SS bond formation. If you don't use the -ss flag with pdb2gmx in GROMACS, the software will not specifically enforce the creation of disulfide bonds based on your instructions. Instead, it may attempt to detect disulfide bonds automatically based on proximity and cysteine residues' geometry within the structure. However, this automatic detection isn't always reliable, especially for complex or ambiguous configurations, which can lead to incorrect or missed disulfide bond formations. NOTE: if CYS forming the bond are not in the same chain, pdb2gmx will not detect it, in this case you need to merge -merge the chains as a previous pdb2gmx step.