MD preview for: Fighting Celiac Disease: Improvement of pH Stability of Cathepsin L In Vitro by Computational Design

Dataset structure:
This is MD preview (some initial and final files, along with light versions of principal MD trajectories) for wild-type (WT) and acidophilic mutant (V277A) cathepsin L versions. Each folder contains three variants of pH calculations:

pH 7

pH 2 (considering all ionizable residues)

pH 2 (considering only His 275)

See paper text for details.

Each subfolder contains seven MD-related files:

md.mdp: Gromacs options file

topol.top: system topology, including ionization states of the charged residues

em.gro: system coordinates before MD

md.gro: system coordinates after MD

md.tpr: Gromacs tpr file required for MD start

md_view.gro: system coordinates after MD without water and ions. Required for MD preview using the next trajectory file

md_view.xtc: "light" MD trajectory file without water and ions with coordinates saved each 100 ps (gmx trjconv "-dt 100" option). Use two latter files for MD preview in software like VMD or Pymol.