example

Example

This folder contains examples of how to use the parna package to model and parameterize RNA molecules. Each subfolder contains a specific example with its own README file that explains how to run the scripts and what the expected output is.

The examples include:

• 00.generate_charge: This example shows how to generate charges for non-canonical nucleotides.
• 01.extract_backbone: This example demonstrates how to extract the backbone of an RNA molecule. This is for the cutomized modeling of chemically modified nucleotides based on a given RNA structure.
• 02.build_structure: This example shows how to construct a customized oligonucleotide from a extracted backbone.
• 03.generate_fep_topology: This example shows how to prepare the FEP simulations. This example requires amberti package.
• 04.parameterize: This example shows how to parameterize a new nucleotide. We also provided the parameters of structures shown in the paper in the Zenodo repo. The output of parameterization is a .yaml file.
• 05.modify_topology: This example shows how to modify an Amber topology file based on a .yaml parameter file.