--AmberTools package version--

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the T4 lysozyme protein (PDB code 3HTB) with two residue modifications L99A/M102Q complexed with the small ligand 2-propylphenol (3-letter code JZ4).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nbcondakernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.

Parameters

Inputs

Parameters needed to configure the workflow:

• pdbCode: PDB code of the protein structure (e.g. 3HTB)
• ligandCode: 3-letter code of the ligand (e.g. JZ4)
• mol_charge: Charge of the ligand (e.g. 0)

Outputs

Output files generated (named according to the input parameters given above):

• output_ions_pdb_path: System structure of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.
• output_free_traj_path: Final trajectory of the MD setup protocol.
• output_free_rst_path: Final checkpoint file, with information about the state of the simulation. It can be used to restart or continue a MD simulation.
• output_ions_top_path: Final topology of the MD system in AMBER Parm7 format.