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L99A T4 Lysozyme (T4L)
T4L has a specific mutation: leucine (L) substitution at position 99 with alanine (A). This change creates a hydrophobic cavity in the C-terminal domain, altering its stability and binding properties (see Figure).
This variant is particularly useful as a model system for studying protein-ligand interactions because the introduced cavity can accommodate small hydrophobic molecules (benzene and its derivatives).
In this tutorial, we will use a structure based on the PDB ID 4w52 with the CHARMM36 force field and run a T4L-benzene dissociation simulation in the NVT ensemble at 300 K using the velocity rescaling thermostat (see the data directory here for more details).