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Common ptraj scripts:

  • hbond.in - A script used with RNA (and modified RNA residues) for hydrogen bond analysis.
  • grid.in - A script to create a grid of average water density in X-Plor format (viewable in Chimera, VMD) with the correct offset for the respective avg.pdb file.
  • combined-clustering.in - Example of combined clustering commands with multiple trajectories (same topology)
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