But 2 of its disulphide bonds out of 5 are missing and I have information on the disulphide bonds and want to include them in to model. I also want to do Molecular dynamics on protein with gromacs. Can some one tell me how can i join the disulphide bonds and do MD?
Open your modelled structure in Discovery studio and from there you build your missing disulfide bond and then minimize the structure then further use this structure for simulation .
If you use Modeller you can use disulphide bonds as initial constrains for the model production (http://salilab.org/modeller/manual/node24.html), then you can proceed for the MD calculations. If you build you S-S bonds after a model that doesn't have then you might placing your protein in a energetic hole were it cannot easily came out of in a EM or MD.
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