aakognole / rna-mg-predictor

Prediction of magnesium binding sites in RNA molecules using GCMC/MD (Updated version: https://github.com/mackerell-lab/GCMC_PME)

rna-mg-predictor

This set of scripts can be used to setup a GCMC-MD simulation to identify the Mg2+ and K+ binding sites in RNA molecules. It has been provided in the form to be applied to native states of RNA, however it was originally designed to study ion-atomsphere during the folding of RNA in following articles.

Kognole AA, MacKerell AD Jr., "Mg2+ Impacts the Twister Ribozyme Through Push- Pull Stabilization of Non-Sequential Phosphate Pairs" Biophysical J. (2020) 118(6): 1424-1437 https://doi.org/10.1016/j.bpj.2020.01.021

Kognole AA,MacKerell AD Jr., "Contributions and Competition of Mg2+ and K+ in Folding and Stabilization of the Twister Ribozyme" RNA (2020) https://doi.org/10.1261/rna.076851.120

You need to have

• GROMACS (https://github.com/gromacs/gromacs)
• OpenMM with CUDA (conda install -c conda-forge openmm)
• Plumed plugin for OpenMM (conda install -c conda-forge openmm-plumed)
• ParmEd to utilize the GROMACS formats in OpenMM (conda install -c omnia parmed)
• MMTSB Toolset to manupulate the PDB files (installed on fly from github)
• MDAnalysis to run clustering analysis ( conda install -c conda-forge mdanalysis)