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How to manually set a disulfide bond in a pdb file?
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+ Gromacs
+ Molecular dynamics simulation
+ Disulfides
+ Protein folding
Posted by
Misaiel Dominguez
How to manually set a disulfide bond in a pdb file?
For the past month, I have been trying to model a tetrameric protein-ligand with a charmm forcefield. Noteworthy is that this protein is held together by disulfide bridges (ssbond). the dynamics of this protein however are very erratic(see rg below).As I verify the trajectories, I have noticed that the disulfide bond is broken for all simulation cases.Is there any way that one can set this s---s bond for my topology?Do I have to modify my pdb file for charmm to understand it?I would like to refer this question to you Dr. Justin Lemkul as you are great expert on the fieldBest regards
