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makson96 / Dynamics

Dynamics PyMOL Plugin
GNU General Public License v3.0
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MD run with interchain disulfide bond #78

Closed clinntt closed 7 years ago

clinntt commented 7 years ago

Hello,

I have tried in a number of ways to run a simulation of two peptides that are bridged with a disulfide bond, but in all cases the plugin breaks the disulfide (forming two cysteines) resulting in the two peptides diffusing away from each other. Even in restrained MD runs, where I have selected the two sulfur atoms as the restraint, the peptides diffuse away. Is there something wrong with my PDB file (attached below)?

Thanks!

Clint Postdoctoral Fellow University of Michigan

tethered_peptides.txt

ghost commented 7 years ago

Hi Clint, Please ask GROMACS community how to correctly set up your simulation. After you acquire such a knowledge, you can then use the plugin to implement it.