(If the formatting of this document looks weird inside your text editor, try turning on "word wrap"). 

Inside this folder is the starting structures and parameter files required to simulate the E8 and AF7 TCRs used as we performed in our study. Below, each folders contents are described.


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0_Starting_Structures
Inside this folder you will find the parameter and topology files used to simulate each system. 

Alongside that, you will see the tleap.in file used to convert the pdb file to the parameter file alongside the specially generated parameters to describe the 5OP-RU unit.


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1_Parameters
Here you can find the parameter files required to simulate the 5OP-RU unit. We have provided a simple 3 residue PDB file that you can use to see how to label the each heavy atom ahead of running tleap.


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2_MD_Inputs
Here you can find the amber MD inputs used to run the md simulations. 
The order of operations is as follows:

minsolv.in 
mdsolv.in 
min.in
heat.in 
npt1.in 
npt2.in
npt3.in
npt4.in
eqnpt.in
prod1.in