Modelling/simulation tools use case, REMD ligand conformations

[adamhospital]

New Use Case

Aspect	Detail
Summary	C1997 (Platforms providing web-access to molecular level tools for guiding systems level modelling)
Usecase Group	Molecular Level
Expert	Adam Hospital, Aurélien Luciani (IRB Barcelona)
Scientific User	Interested in ligand conformations
Deadline	M22
Target audience	New users of molecular modelling/simulation tools
Target interface	GUI and notebooks (latter for tutorials)
HPC Requirements	none
Dependencies	nglview, GROMACS, BioExcel building blocks library (biobb), ACPype, Ambertools, OpenBabel
Nominal runtime	~1h

Use case : Generating small molecule conformations from Replica Exchange Molecular Dynamics (REMD)

Running a Replica Exchange Molecular Dynamics (REMD) for a small molecule in PDB format to obtain an ensemble of conformations ready to be used as input for docking simulations. Extending the "Small molecule force field parametrization for atomistic Molecular Dynamics simulations" notebook. Using GROMACS MD package and the building blocks library from the BioExcel project.

Mandatory features

• Takes as input a PDB format file describing the 3D atomic structure of a small molecule.
• Model hydrogen atoms from a desired pH.
• Energetically minimize the molecule with the newly added atoms.
• Generate the force field parameters (GAFF) using ACPype.
• Add solvent box surrounding the system.
• Add counter ions to neutralize the charge and/or reach a desired ionic concentration.
• Energetically equilibrate the whole system (molecule + solvent + ions).
• Run a short free MD simulation to check for a correct system equilibration.
• Run a REMD with a desired temperature range (e.g. 270K to 600K).
• Extract a representative ensemble from the resulting trajectories.

Important features

• Visualize the intermediate structures using nglview jupyter widget.

To do

• [ ] Create the jupyter notebook with all the required dependencies.
• [ ] Write markdown cells with information about the workflow and the different steps.
• [ ] Test the workflow with different input small molecules.
• [ ] Make the notebook publicly available.

[alex4200]

Still in progress, but delayed as Aurélien left the group two months ago. Might be moved to SGA3