In order to reduce the influence between domains that can cause dimerization in MD simulations through biosensor structures, FL biosensors were isolated, structural prediction was performed with Alpha Fold 2, and MD was performed with Gromacs.
Now I want to put two PDB files together from the trajectory file, including the situation of a specific frame, and restore them back to a single intact protein. I divided the front and back based on a specific part of the linker domain. How can I put two proteins back together into a single PDB file?
It would be nice if I could use the built-in functionality of GUI tools such as pymol or the additional plug-in to proceed with the work.
If you have a full version of pymol, you can drag one part and bring it closer to second part.
In Chimera, you need to edit the PDB to make them two PDB molecules, and then you can rotate one molecule with respect to another (Tools -> model section, I think). You can google it.
This means that during the simulation, your molecule drifted into the periodic boundary box. See here https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow to learn how to fix this in gromacs
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