Molecular Dynamics Trajectories of Membrane-bound Influenza Hemagglutinin (A/duck/Alberta/35/76) in Complex with 0-3 Copies of FISW84 Fab Fragments

MD simulation trajectories of influenza hemagglutinin (A/duck/Alberta/35/76) in a bilayer mimicking the viral membrane, with 0-3 copies of FISW84 antibody's Fab domains bound.

Files are named as (copy number of Fab).(simulation replica ID).(file type extension). The systems were constructed in CHARMM format PSF files and the trajectories were recorded in DCD format.

Simulations were performed with NAMD3. The trajectories were re-centered and re-wrapped about the periodic boundary from the raw trajectories, in order to keep the HA-Fab complex and the lipid bilayer appearing as a single continuous entity instead of isolated molecules at the opposite side of the periodic boundary. Water molecules in the simulation were removed in these trajectories due to file size limitations.