The directory structure goes as follows

1. ligand of choice (all use the same neuraminidase protein)
#for example, oseltamivir

2. ligand conformation
#only applicable to sialic acid

3. glycan conformation
#these conformations come from the molecular dynamics simulations - conformation 1 is the most accessed conformation, conformation 2 is the second most accessed, and so on. Static are the conformations from the glyprot web server. 

4. binding site
#primary is the primary, catalytic site; secondary is the secondary site; combined uses both sites as potential end points for the Browian dynamics trajectories

5. glycan presence
#redundant, not much to see here

6. type of trajectory
#all use nam_simulation, weighted ensemble was not used after irregularities were found during testing

7. final files and their outputs
#the input files you need to rerun these trajectories are the protein.in, protein.pqr, input.xml, ligand.in, ligand.pqr, rxns*.xml. From these you can create the .dx files and all the other ancillary files needed; then you can run this with nam_simulation to generate the output files seen here.
#note, some of these output files are ones from additional tests where parameters were changed and may not reflect the data in the paper. An example of this would be changing the association distance in the rxn*.xml file from the paper's distance to some other distance. Reverting this distance in the file and rerunning would take 1-2 days and would generate new output files that relect the data in the paper.