Making Disulfide Bonds

The easiest way to do this is by using the mechanism implemented with the specbond.dat file and pdb2gmx. You may find pdb2gmx -ss yes is useful. The sulfur atoms will need to be in the same unit that pdb2gmx is converting to a moleculetype, so invoking pdb2gmx -chainsep correctly may be required. See pdb2gmx -h. This requires that the two sulfur atoms be within a distance + tolerance (usually 10%) in order to be recognised as a disulfide. If your sulfur atoms are not this close, then either you can

• edit the contents of specbond.dat to allow the bond formation and do energy minimization very carefully to allow the bond to relax to a sensible length, or
• run a preliminary EM or MD with a distance restraint (and no disulfide bond) between these sulfur atoms with a large force constant so that they approach within the existing specbond.dat range to provide a suitable coordinate file for a second invocation of pdb2gmx.

Otherwise, editing your .top file by hand is the only option.