Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from Theophylline-Binding RNA Aptamer

This repository contains input files, execution, and analysis scripts for free energy calculations performed for our manuscript titled "Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from Theophylline-Binding RNA Aptamer" Rasouli et al. 2024.

Contact

Mehtap Işık Bennett ([email protected])

Contributors

• Ali Rasouli (ORCID: 0000-0002-0313-0236)
• Frank C. Pickard IV (ORCID: 0000-0002-9608-3466)
• Sreyoshi Sur (ORCID: 0000-0001-7780-2640)
• Alan Grossfield (ORCID: 0000-0002-5877-2789)
• Mehtap Işık Bennett (ORCID: 0000-0002-6789-952X)

Contents

• fe_calcs_with_0_or_2_mg/ - Directory for free energy calculations of Theophylline binding aptamer with zero or two structural Mg+2 ions
• fe_calcs_with_3_mg/ - Directory for free energy calculations of Theophylline binding aptamer with zero or two structural Mg+2 ions
• mmgbsa_calc_with_0_or_2_mg/ - Directory for MM-GBSA calculations
• ligands/ - Directory for SDF files of Theopylline analogs